![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Last modified 11 months ago
#17037 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001f9a78f80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 65)
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "Mac14,6",
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"build" : "23H311",
"releaseType" : "User"
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"captureTime" : "2025-03-06 17:49:00.4435 -0500",
"codeSigningMonitor" : 1,
"incident" : "7DED01CE-C246-46FC-9134-EC9AC0D28D36",
"pid" : 16551,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-19 16:33:07.8962 -0500",
"procStartAbsTime" : 29253478198556,
"procExitAbsTime" : 38029001375900,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"33683ED1-4295-506E-98C7-0A45107A4F52","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2004EEB0-6CE4-B69C-55BC-8DB5DE4ACC9C",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 28391,
"sleepWakeUUID" : "F8E2DF71-97C3-4CF0-9AE8-90E40F81A0FF",
"sip" : "enabled",
"vmRegionInfo" : "0xffff81276816b30e is not in any region. Bytes after previous region: 18446499047034761999 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600100000000-600120000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x9ab601276816b30e","rawCodes":[1,-7298644877345639666],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x9ab601276816b30e -> 0xffff81276816b30e (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":16551},
"vmregioninfo" : "0xffff81276816b30e is not in any region. Bytes after previous region: 18446499047034761999 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600100000000-600120000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> set bgColor white
> graphics silhouettes true
> alias newcolor color $1 darkseagreen ; color $2 burlywood ; color $3 coral ;
> color $4 #498cff ; color $5 mediumslateblue ; color $6 grey ; color $7
> #ff69b4 ; color $8 #20B2AA ; color $9 #20B2AA
> alias propercolor color $1 mediumslateblue ; color $2 lightcoral ; color $3
> darkseagreen ; color $4 burlywood ; color $5 coral ; color $6 grey ; color
> $7 #bb57a1ff ; color $8 #0080ffff ; color $9 #004080ff
> alias removeatom select main ; style stick ; color sel byhetero ; hide sel
> atoms ; show sel cartoons ; select clear
> alias showATP select ::name="ATP" ; show sel ; color sel byhetero ; select
> clear
> alias modelfix style stick ; newcolor /A /B /C /D /E /F /G /H /I ; color
> byhetero ; show cartoons ; select clear ; select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
> ; hide sel atoms ; select clear
> lighting soft
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/apo_ylORC1-6_autoinhibited_O1AAA/fragmented from
> 2.3A map/apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc"
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc as #1, grid size
100,75,99, pixel 0.827,0.827,0.827, shown at level 0.351, step 1, values
float32
> volume #1 level 0.09834
> volume #1 level 0.1
> ui mousemode right "map eraser"
> volume erase #1 center 163.89,176.39,145.09 radius 12.448
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy as #3, grid size
100,75,99, pixel 0.827,0.827,0.827, shown at step 1, values float32
> volume erase #3 center 160.72,178.6,147.14 radius 25.099
> volume erase #3 center 153.84,165.37,159.35 radius 25.099
> volume erase #3 center 186.28,218.17,168.98 radius 18.318
> volume erase #3 center 177.17,206.22,131.59 radius 34.403
> volume erase #3 center 218.68,194.01,175.8 radius 34.403
> volume erase #3 center 189.93,162.62,149.15 radius 34.403
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/ylODC_54bp-
> oriC061_complete/ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc"
Opened ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc as #2, grid size 440,440,440,
pixel 0.827, shown at level 0.0339, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-6.5437,0,1,0,-39.682,0,0,1,32.694
> view matrix models #3,1,0,0,63.882,0,1,0,-59.979,0,0,1,-62.393
> view matrix models #3,1,0,0,38.347,0,1,0,-95.198,0,0,1,-13.033
> view matrix models #3,1,0,0,16.509,0,1,0,-66.14,0,0,1,-0.99619
> view matrix models #3,1,0,0,20.128,0,1,0,-62.33,0,0,1,-2.0463
> close #1
> fitmap #3 inMap #2
Fit map apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy in map
ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc using 11600 points
correlation = 0.9405, correlation about mean = 0.5992, overlap = 241.7
steps = 200, shift = 2.29, angle = 36.2 degrees
Position of apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy (#3)
relative to ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.84572459 -0.49295295 0.20432158 104.99315114
0.53093078 0.81572589 -0.22957303 -70.02432300
-0.05350170 0.30263617 0.95160334 -43.34359941
Axis 0.45011126 0.21805178 0.86594069
Axis point 185.17878159 160.09585855 0.00000000
Rotation angle (degrees) 36.24202405
Shift along axis -5.54331477
> ui mousemode right select
> select clear
> vop resample #3 onGrid #2
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled as #1,
grid size 440,440,440, pixel 0.827, shown at step 1, values float32
> volume #1 level 0.0764
> volume #1 level 0.1
> volume #1 level 0.15
> volume #2 level 0.05442
> volume #2 level 0.1
> select #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99933,-0.018848,0.031243,-3.0076,0.018589,0.99979,0.0085722,-4.9693,-0.031398,-0.0079858,0.99948,6.9845
> fitmap #3 inMap #2
Fit map apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy in map
ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc using 11600 points
correlation = 0.9405, correlation about mean = 0.5991, overlap = 241.7
steps = 160, shift = 0.0161, angle = 0.0151 degrees
Position of apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy (#3)
relative to ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.84577508 -0.49297133 0.20406808 105.02263727
0.53087390 0.81574712 -0.22962913 -70.01411447
-0.05326738 0.30254901 0.95164420 -43.38215291
Axis 0.45014347 0.21766749 0.86602062
Axis point 185.20083727 160.15397652 0.00000000
Rotation angle (degrees) 36.23656846
Shift along axis -5.53438078
> ui mousemode right select
> select #3
2 models selected
> volume #3 level 0.15
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select clear
> close #1
> vop resample #3 onGrid #2
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled as #1,
grid size 440,440,440, pixel 0.827, shown at step 1, values float32
> volume #1 level 0.2
> volume #1 level 0.15
> vop flip #1
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled z flip
as #4, grid size 440,440,440, pixel 0.827, shown at step 1, values float32
> vop flip #2
Opened ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc z flip as #5, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
> save /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/High-Res-ORC2WHD-
> mask_BASE_notBinary.mrc models #4
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/cryosparc_frame4_J411_003_volume_map.mrc"
Opened cryosparc_frame4_J411_003_volume_map.mrc as #6, grid size 440,440,440,
pixel 0.827, shown at level 0.0169, step 2, values float32
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/frame2_J413.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/cryosparc_P370_J410_005_volume_map.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/cryosparc_frame4_J411_003_volume_map.mrc"
Opened frame2_J413.mrc as #1.1, grid size 440,440,440, pixel 0.827, shown at
level 0.022, step 2, values float32
Opened cryosparc_P370_J410_005_volume_map.mrc as #1.2, grid size 440,440,440,
pixel 0.827, shown at level 0.019, step 2, values float32
Opened cryosparc_frame4_J411_003_volume_map.mrc as #1.3, grid size
440,440,440, pixel 0.827, shown at level 0.0169, step 2, values float32
> vop step 1
> vop level 0.1
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/ylORC1-6_oriC061_OPEN_noO1AAA/ORC-
> OPEN_DNA_P370_J167_FLIPPED.mrc"
Opened ORC-OPEN_DNA_P370_J167_FLIPPED.mrc as #2, grid size 440,440,440, pixel
0.827, shown at level 0.0182, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1
> vop flip #1
Opened frame2_J413.mrc z flip as #3, grid size 440,440,440, pixel 0.827, shown
at step 1, values float32
Opened cryosparc_P370_J410_005_volume_map.mrc z flip as #4, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened cryosparc_frame4_J411_003_volume_map.mrc z flip as #5, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
> close #1#1.1-3
> fitmap #3 inMap #2
Fit map frame2_J413.mrc z flip in map ORC-OPEN_DNA_P370_J167_FLIPPED.mrc using
209824 points
correlation = 0.8749, correlation about mean = 0.6459, overlap = 5044
steps = 348, shift = 6.71, angle = 15.5 degrees
Position of frame2_J413.mrc z flip (#3) relative to ORC-
OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.97446697 0.02860606 0.22270119 -35.49808469
0.00472647 0.98901775 -0.14772120 23.54512380
-0.22448115 0.14500202 0.96362992 17.88035991
Axis 0.54714223 0.83584876 -0.04463441
Axis point 52.95063289 0.00000000 164.14097100
Rotation angle (degrees) 15.51567190
Shift along axis -0.54041832
> fitmap #4 inMap #2
Fit map cryosparc_P370_J410_005_volume_map.mrc z flip in map ORC-
OPEN_DNA_P370_J167_FLIPPED.mrc using 160211 points
correlation = 0.9112, correlation about mean = 0.6738, overlap = 4054
steps = 220, shift = 2.82, angle = 8.58 degrees
Position of cryosparc_P370_J410_005_volume_map.mrc z flip (#4) relative to
ORC-OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.99234355 -0.00562414 0.12338008 -16.99642910
0.01597062 0.99641901 -0.08303075 10.54881173
-0.12247128 0.08436548 0.98887980 8.05853927
Axis 0.56133195 0.82441655 0.07241400
Axis point 53.25288131 0.00000000 139.87627102
Rotation angle (degrees) 8.57513729
Shift along axis -0.26047268
> fitmap #5 inMap #2
Fit map cryosparc_frame4_J411_003_volume_map.mrc z flip in map ORC-
OPEN_DNA_P370_J167_FLIPPED.mrc using 154100 points
correlation = 0.9198, correlation about mean = 0.6573, overlap = 4122
steps = 120, shift = 1.21, angle = 4.97 degrees
Position of cryosparc_frame4_J411_003_volume_map.mrc z flip (#5) relative to
ORC-OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.99738968 -0.01045075 0.07144651 -9.18473790
0.01387007 0.99877345 -0.04753118 5.34475067
-0.07086214 0.04839807 0.99631129 4.38863766
Axis 0.55342664 0.82099463 0.14030953
Axis point 55.32397495 0.00000000 129.96106991
Rotation angle (degrees) 4.97197356
Shift along axis -0.07929937
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!5 models
> hide #!2 models
> show #!4 models
> show #!3 models
> hide #!5 models
> volume #3 level 0.171
> volume #4 level 0.1381
> volume #4 level 0.1
> volume #3 level 0.1
> hide #!3 models
> show #!3 models
> volume #3 level 0.1121
> volume #3 level 0.08
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylORC1-6_oriC061_closed_noO1AAA/ORC-DNA-closed-
> noCdc6-noO1AAA_rev2_sidechains-not-done.pdb"
Chain information for ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not-
done.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
> modelfix
Changed 18185 atom styles
16772 atoms, 17104 bonds, 8 pseudobonds, 2086 residues, 2 models selected
> hide #!1 models
> show #!1 models
> fitmap #1 inMap #3
Fit molecule ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not-done.pdb (#1)
to map frame2_J413.mrc z flip (#3) using 18185 atoms
average map value = 0.1748, steps = 108
shifted from previous position = 3.5
rotated from previous position = 6.13 degrees
atoms outside contour = 2411, contour level = 0.08
Position of ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not-done.pdb (#1)
relative to frame2_J413.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99078521 -0.01123591 -0.13497562 25.44161891
0.02375867 0.99551894 0.09152899 -17.35760278
0.13334237 -0.09389241 0.98661240 -3.43448090
Axis -0.56526644 -0.81798084 0.10668273
Axis point 43.71104119 0.00000000 183.20504019
Rotation angle (degrees) 9.43986719
Shift along axis -0.54950672
> select /C:220
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:157
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:171
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> volume #3 level 0.06943
> close #1
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev29_PostPhenix.pdb"
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 25299 atom styles
23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected
> fitmap #1 inMap #3
Fit molecule ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) to map
frame2_J413.mrc z flip (#3) using 25299 atoms
average map value = 0.124, steps = 184
shifted from previous position = 4.41
rotated from previous position = 6.1 degrees
atoms outside contour = 9398, contour level = 0.06943
Position of ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) relative to
frame2_J413.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99093954 -0.00429549 -0.13423996 23.99797706
0.01699922 0.99546171 0.09363235 -16.70012343
0.13322855 -0.09506597 0.98651539 -3.03142526
Axis -0.57525720 -0.81539242 0.06491808
Axis point 40.21853239 0.00000000 174.40638339
Rotation angle (degrees) 9.43985245
Shift along axis -0.38464920
> select /D:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> volume #3 level 0.06037
> select clear
Unsupported scale factor (0.000000) detected on Display0
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-
> maps/apo_ylORC1-6_autoinhibited_O1AAA/cryosparc_P370_J421_map_sharp.mrc"
Opened cryosparc_P370_J421_map_sharp.mrc as #6, grid size 480,480,480, pixel
0.84, shown at level 0.0726, step 2, values float32
> hide #!1 models
> volume #6 step 1
> volume #6 level 0.1165
> volume #6 level 0.2042
> vop flip #6
Opened cryosparc_P370_J421_map_sharp.mrc z flip as #7, grid size 480,480,480,
pixel 0.84, shown at step 1, values float32
> close #6
> volume #7 level 0.2919
> volume #7 level 0.2656
> close #7
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_024.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_023.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_022.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_021.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_020.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_019.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_018.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_017.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_016.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_015.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_014.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_013.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_012.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_011.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_010.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_009.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_008.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_007.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_006.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_005.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_004.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_003.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_002.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_001.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_000.mrc"
Opened J407_component_000_frame_024.mrc as #1.1, grid size 440,440,440, pixel
0.827, shown at level 0.0246, step 2, values float32
Opened J407_component_000_frame_023.mrc as #1.2, grid size 440,440,440, pixel
0.827, shown at level 0.0247, step 2, values float32
Opened J407_component_000_frame_022.mrc as #1.3, grid size 440,440,440, pixel
0.827, shown at level 0.0246, step 2, values float32
Opened J407_component_000_frame_021.mrc as #1.4, grid size 440,440,440, pixel
0.827, shown at level 0.0248, step 2, values float32
Opened J407_component_000_frame_020.mrc as #1.5, grid size 440,440,440, pixel
0.827, shown at level 0.025, step 2, values float32
Opened J407_component_000_frame_019.mrc as #1.6, grid size 440,440,440, pixel
0.827, shown at level 0.0253, step 2, values float32
Opened J407_component_000_frame_018.mrc as #1.7, grid size 440,440,440, pixel
0.827, shown at level 0.0256, step 2, values float32
Opened J407_component_000_frame_017.mrc as #1.8, grid size 440,440,440, pixel
0.827, shown at level 0.0259, step 2, values float32
Opened J407_component_000_frame_016.mrc as #1.9, grid size 440,440,440, pixel
0.827, shown at level 0.0262, step 2, values float32
Opened J407_component_000_frame_015.mrc as #1.10, grid size 440,440,440, pixel
0.827, shown at level 0.0265, step 2, values float32
Opened J407_component_000_frame_014.mrc as #1.11, grid size 440,440,440, pixel
0.827, shown at level 0.0267, step 2, values float32
Opened J407_component_000_frame_013.mrc as #1.12, grid size 440,440,440, pixel
0.827, shown at level 0.0268, step 2, values float32
Opened J407_component_000_frame_012.mrc as #1.13, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_000_frame_011.mrc as #1.14, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_000_frame_010.mrc as #1.15, grid size 440,440,440, pixel
0.827, shown at level 0.0268, step 2, values float32
Opened J407_component_000_frame_009.mrc as #1.16, grid size 440,440,440, pixel
0.827, shown at level 0.0266, step 2, values float32
Opened J407_component_000_frame_008.mrc as #1.17, grid size 440,440,440, pixel
0.827, shown at level 0.0265, step 2, values float32
Opened J407_component_000_frame_007.mrc as #1.18, grid size 440,440,440, pixel
0.827, shown at level 0.0263, step 2, values float32
Opened J407_component_000_frame_006.mrc as #1.19, grid size 440,440,440, pixel
0.827, shown at level 0.0261, step 2, values float32
Opened J407_component_000_frame_005.mrc as #1.20, grid size 440,440,440, pixel
0.827, shown at level 0.026, step 2, values float32
Opened J407_component_000_frame_004.mrc as #1.21, grid size 440,440,440, pixel
0.827, shown at level 0.0258, step 2, values float32
Opened J407_component_000_frame_003.mrc as #1.22, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_002.mrc as #1.23, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_001.mrc as #1.24, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_000.mrc as #1.25, grid size 440,440,440, pixel
0.827, shown at level 0.0258, step 2, values float32
> vop step 1
> vop level 0.1
> fitmap #1.2 inMap #1.1
Fit map J407_component_000_frame_023.mrc in map
J407_component_000_frame_024.mrc using 209250 points
correlation = 0.9997, correlation about mean = 0.998, overlap = 8175
steps = 44, shift = 0.00683, angle = 0.0107 degrees
Position of J407_component_000_frame_023.mrc (#1.2) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999999 -0.00012647 -0.00005333 0.03293876
0.00012647 0.99999998 0.00012643 -0.05198641
0.00005331 -0.00012643 0.99999999 0.01305327
Axis -0.67751845 -0.28572825 0.67773749
Axis point 407.94854492 267.83546595 0.00000000
Rotation angle (degrees) 0.01069187
Shift along axis 0.00138407
> fitmap #1.3 inMap #1.1
Fit map J407_component_000_frame_022.mrc in map
J407_component_000_frame_024.mrc using 203717 points
correlation = 0.9986, correlation about mean = 0.9908, overlap = 7802
steps = 40, shift = 0.0172, angle = 0.0261 degrees
Position of J407_component_000_frame_022.mrc (#1.3) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999990 -0.00019261 -0.00039264 0.12474433
0.00019266 0.99999997 0.00012757 -0.06314784
0.00039262 -0.00012765 0.99999991 -0.04255682
Axis -0.28010520 -0.86182612 0.42284371
Axis point 110.06260037 0.00000000 318.73939640
Rotation angle (degrees) 0.02610266
Shift along axis 0.00148604
> fitmap #1.4 inMap #1.1
Fit map J407_component_000_frame_021.mrc in map
J407_component_000_frame_024.mrc using 198335 points
correlation = 0.9964, correlation about mean = 0.9756, overlap = 7418
steps = 44, shift = 0.0346, angle = 0.0352 degrees
Position of J407_component_000_frame_021.mrc (#1.4) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999985 -0.00028033 -0.00047313 0.15686283
0.00028046 0.99999992 0.00027270 -0.11547011
0.00047306 -0.00027283 0.99999985 -0.00564243
Axis -0.44433259 -0.77067092 0.45676569
Axis point 28.17446960 0.00000000 347.22791612
Rotation angle (degrees) 0.03517232
Shift along axis 0.01671292
> fitmap #1.5 inMap #1.1
Fit map J407_component_000_frame_020.mrc in map
J407_component_000_frame_024.mrc using 193267 points
correlation = 0.9926, correlation about mean = 0.9494, overlap = 7047
steps = 60, shift = 0.0446, angle = 0.0543 degrees
Position of J407_component_000_frame_020.mrc (#1.5) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999970 -0.00057369 -0.00052292 0.22913926
0.00057398 0.99999969 0.00054339 -0.22570178
0.00052261 -0.00054369 0.99999972 0.04101180
Axis -0.57357699 -0.55165719 0.60554420
Axis point 376.23364392 417.12641997 0.00000000
Rotation angle (degrees) 0.05429535
Shift along axis 0.01791546
> fitmap #1.6 inMap #1.1
Fit map J407_component_000_frame_019.mrc in map
J407_component_000_frame_024.mrc using 188984 points
correlation = 0.9863, correlation about mean = 0.9083, overlap = 6678
steps = 48, shift = 0.0575, angle = 0.0736 degrees
Position of J407_component_000_frame_019.mrc (#1.6) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999937 -0.00074520 -0.00084161 0.32749078
0.00074572 0.99999953 0.00062002 -0.28019774
0.00084115 -0.00062065 0.99999945 0.00597028
Axis -0.48315481 -0.65532311 0.58061438
Axis point 13.08513741 0.00000000 405.67912733
Rotation angle (degrees) 0.07356325
Shift along axis 0.02885774
> fitmap #1.7 inMap #1.1
Fit map J407_component_000_frame_018.mrc in map
J407_component_000_frame_024.mrc using 185458 points
correlation = 0.976, correlation about mean = 0.8493, overlap = 6310
steps = 48, shift = 0.0664, angle = 0.101 degrees
Position of J407_component_000_frame_018.mrc (#1.7) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999880 -0.00101281 -0.00116866 0.44242428
0.00101380 0.99999913 0.00084596 -0.38421046
0.00116780 -0.00084714 0.99999896 -0.01109545
Axis -0.48017506 -0.66263457 0.57475851
Axis point 27.45801527 0.00000000 393.24528287
Rotation angle (degrees) 0.10101276
Shift along axis 0.03577283
> fitmap #1.8 inMap #1.1
Fit map J407_component_000_frame_017.mrc in map
J407_component_000_frame_024.mrc using 183289 points
correlation = 0.9601, correlation about mean = 0.7729, overlap = 5913
steps = 48, shift = 0.0993, angle = 0.147 degrees
Position of J407_component_000_frame_017.mrc (#1.8) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999771 -0.00151197 -0.00151334 0.63051172
0.00151411 0.99999786 0.00140855 -0.58580425
0.00151121 -0.00141083 0.99999786 0.05858363
Axis -0.55024534 -0.59028684 0.59058573
Axis point 374.46052800 428.62087361 0.00000000
Rotation angle (degrees) 0.14678795
Shift along axis 0.03345506
> fitmap #1.9 inMap #1.1
Fit map J407_component_000_frame_016.mrc in map
J407_component_000_frame_024.mrc using 182675 points
correlation = 0.9355, correlation about mean = 0.6834, overlap = 5515
steps = 60, shift = 0.127, angle = 0.201 degrees
Position of J407_component_000_frame_016.mrc (#1.9) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999541 -0.00199889 -0.00227570 0.88265488
0.00200291 0.99999644 0.00176426 -0.75951590
0.00227217 -0.00176881 0.99999585 0.00414204
Axis -0.50380000 -0.64850507 0.57063713
Axis point 11.52035137 0.00000000 398.95768312
Rotation angle (degrees) 0.20090381
Shift along axis 0.05023198
> fitmap #1.10 inMap #1.1
Fit map J407_component_000_frame_015.mrc in map
J407_component_000_frame_024.mrc using 183507 points
correlation = 0.9007, correlation about mean = 0.5875, overlap = 5095
steps = 64, shift = 0.173, angle = 0.289 degrees
Position of J407_component_000_frame_015.mrc (#1.10) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999101 -0.00276858 -0.00321317 1.22924900
0.00277736 0.99999241 0.00273204 -1.11683070
0.00320558 -0.00274094 0.99999111 0.04432005
Axis -0.54214099 -0.63582814 0.54936848
Axis point -1.07295593 0.00000000 394.04766813
Rotation angle (degrees) 0.28920482
Shift along axis 0.06803416
> fitmap #1.11 inMap #1.1
Fit map J407_component_000_frame_014.mrc in map
J407_component_000_frame_024.mrc using 185464 points
correlation = 0.8576, correlation about mean = 0.4935, overlap = 4658
steps = 68, shift = 0.257, angle = 0.451 degrees
Position of J407_component_000_frame_014.mrc (#1.11) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99997838 -0.00387997 -0.00530947 1.90413629
0.00390287 0.99998310 0.00431009 -1.66245856
0.00529266 -0.00433072 0.99997662 0.00352928
Axis -0.54908908 -0.67372352 0.49456830
Axis point 8.07677421 0.00000000 366.48177817
Rotation angle (degrees) 0.45082580
Shift along axis 0.07624247
> fitmap #1.12 inMap #1.1
Fit map J407_component_000_frame_013.mrc in map
J407_component_000_frame_024.mrc using 188095 points
correlation = 0.8117, correlation about mean = 0.4088, overlap = 4242
steps = 72, shift = 0.438, angle = 0.846 degrees
Position of J407_component_000_frame_013.mrc (#1.12) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99992647 -0.00628818 -0.01036874 3.45771106
0.00637521 0.99994455 0.00838211 -2.99419606
0.01031546 -0.00844760 0.99991111 -0.07122117
Axis -0.57011020 -0.70068168 0.42897500
Axis point 13.82106219 -0.00000000 338.66317537
Rotation angle (degrees) 0.84571953
Shift along axis 0.09614987
> fitmap #1.13 inMap #1.1
Fit map J407_component_000_frame_012.mrc in map
J407_component_000_frame_024.mrc using 190432 points
correlation = 0.826, correlation about mean = 0.4787, overlap = 4037
steps = 116, shift = 2.59, angle = 5.32 degrees
Position of J407_component_000_frame_012.mrc (#1.13) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99693363 -0.00485375 -0.07810112 18.39674331
0.00874835 0.99873077 0.04960155 -12.12187935
0.07776124 -0.05013271 0.99571075 -3.59284498
Axis -0.53753568 -0.84004816 0.07331093
Axis point 59.10885375 0.00000000 233.44064050
Rotation angle (degrees) 5.32297724
Shift along axis 0.03066174
> fitmap #1.14 inMap #1.1
Fit map J407_component_000_frame_011.mrc in map
J407_component_000_frame_024.mrc using 192986 points
correlation = 0.8264, correlation about mean = 0.5097, overlap = 4134
steps = 180, shift = 3.25, angle = 6.55 degrees
Position of J407_component_000_frame_011.mrc (#1.14) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99536641 -0.00257223 -0.09612019 22.16708898
0.00847171 0.99810069 0.06101846 -14.42324176
0.09578068 -0.06155003 0.99349769 -4.19909428
Axis -0.53764860 -0.84177617 0.04844440
Axis point 59.32007584 0.00000000 227.86856058
Rotation angle (degrees) 6.54512439
Shift along axis 0.01961419
> vop flip #1
Opened J407_component_000_frame_024.mrc z flip as #2, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_023.mrc z flip as #3, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_022.mrc z flip as #4, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_021.mrc z flip as #5, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_020.mrc z flip as #6, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_019.mrc z flip as #7, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_018.mrc z flip as #8, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_017.mrc z flip as #9, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_016.mrc z flip as #10, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_015.mrc z flip as #11, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_014.mrc z flip as #12, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_013.mrc z flip as #13, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_012.mrc z flip as #14, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_011.mrc z flip as #15, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_010.mrc z flip as #16, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_009.mrc z flip as #17, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_008.mrc z flip as #18, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_007.mrc z flip as #19, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_006.mrc z flip as #20, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_005.mrc z flip as #21, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_004.mrc z flip as #22, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_003.mrc z flip as #23, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_002.mrc z flip as #24, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_001.mrc z flip as #25, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_000.mrc z flip as #26, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
> close #1
> fitmap #3 inMap #2
Fit map J407_component_000_frame_023.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 209250 points
correlation = 0.9997, correlation about mean = 0.998, overlap = 8159
steps = 44, shift = 0.0122, angle = 0.0166 degrees
Position of J407_component_000_frame_023.mrc z flip (#3) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999998 -0.00007198 0.00017080 -0.01218363
0.00007199 1.00000000 -0.00004990 -0.01272519
-0.00017079 0.00004991 0.99999998 0.00861980
Axis 0.26000175 0.88979882 0.37504286
Axis point 75.18576895 0.00000000 54.20442455
Rotation angle (degrees) 0.01099771
Shift along axis -0.01125783
> fitmap #4 inMap #2
Fit map J407_component_000_frame_022.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 203717 points
correlation = 0.9986, correlation about mean = 0.9908, overlap = 7804
steps = 44, shift = 0.00922, angle = 0.043 degrees
Position of J407_component_000_frame_022.mrc z flip (#4) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999993 -0.00018708 0.00032120 -0.00987873
0.00018712 0.99999998 -0.00010622 -0.01960247
-0.00032118 0.00010628 0.99999994 0.03150743
Axis 0.27483331 0.83080943 0.48396524
Axis point 103.74870000 0.00000000 27.56737164
Rotation angle (degrees) 0.02215041
Shift along axis -0.00375242
> fitmap #5 inMap #2
Fit map J407_component_000_frame_021.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 198335 points
correlation = 0.9964, correlation about mean = 0.9756, overlap = 7433
steps = 48, shift = 0.0353, angle = 0.0607 degrees
Position of J407_component_000_frame_021.mrc z flip (#5) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999983 -0.00035430 0.00045957 -0.00246458
0.00035440 0.99999991 -0.00022596 -0.04001364
-0.00045949 0.00022612 0.99999987 0.02969192
Axis 0.36297181 0.73789422 0.56900227
Axis point 81.37020887 0.00000000 -5.29006039
Rotation angle (degrees) 0.03568139
Shift along axis -0.01352564
> fitmap #6 inMap #2
Fit map J407_component_000_frame_020.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 193267 points
correlation = 0.9926, correlation about mean = 0.9494, overlap = 7051
steps = 48, shift = 0.0572, angle = 0.091 degrees
Position of J407_component_000_frame_020.mrc z flip (#6) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999963 -0.00049347 0.00070005 -0.00617347
0.00049379 0.99999977 -0.00046712 -0.02146966
-0.00069982 0.00046747 0.99999965 0.00864692
Axis 0.47894449 0.71738422 0.50593682
Axis point 22.46606534 -0.00000000 -0.73683347
Rotation angle (degrees) 0.05590211
Shift along axis -0.01398395
> fitmap #7 inMap #2
Fit map J407_component_000_frame_019.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 188984 points
correlation = 0.9863, correlation about mean = 0.9084, overlap = 6677
steps = 44, shift = 0.0751, angle = 0.121 degrees
Position of J407_component_000_frame_019.mrc z flip (#7) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999936 -0.00073951 0.00086022 0.01917742
0.00074004 0.99999953 -0.00062080 -0.05247554
-0.00085976 0.00062143 0.99999944 -0.00306149
Axis 0.48025379 0.66495781 0.57200298
Axis point 14.71644850 0.00000000 -37.59932412
Rotation angle (degrees) 0.07410093
Shift along axis -0.02743518
> fitmap #8 inMap #2
Fit map J407_component_000_frame_018.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 185458 points
correlation = 0.976, correlation about mean = 0.8495, overlap = 6307
steps = 48, shift = 0.0762, angle = 0.166 degrees
Position of J407_component_000_frame_018.mrc z flip (#8) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999889 -0.00109466 0.00101112 0.06239608
0.00109572 0.99999885 -0.00105131 -0.05426405
-0.00100997 0.00105242 0.99999894 -0.06011444
Axis 0.57667175 0.55401943 0.60042665
Axis point 34.34276710 72.86216565 0.00000000
Rotation angle (degrees) 0.10450891
Shift along axis -0.03017559
> fitmap #9 inMap #2
Fit map J407_component_000_frame_017.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 183289 points
correlation = 0.9601, correlation about mean = 0.7729, overlap = 5915
steps = 64, shift = 0.122, angle = 0.236 degrees
Position of J407_component_000_frame_017.mrc z flip (#9) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999771 -0.00148690 0.00153937 0.06533420
0.00148900 0.99999796 -0.00136750 -0.08041576
-0.00153733 0.00136979 0.99999788 -0.04587663
Axis 0.53874971 0.60555051 0.58571096
Axis point -14.38402550 0.00000000 -56.59152311
Rotation angle (degrees) 0.14555510
Shift along axis -0.04036747
> fitmap #10 inMap #2
Fit map J407_component_000_frame_016.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 182675 points
correlation = 0.9352, correlation about mean = 0.6832, overlap = 5522
steps = 52, shift = 0.145, angle = 0.328 degrees
Position of J407_component_000_frame_016.mrc z flip (#10) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999558 -0.00205030 0.00215508 0.07345453
0.00205433 0.99999614 -0.00186887 -0.11702549
-0.00215124 0.00187329 0.99999593 -0.03493961
Axis 0.53244610 0.61271628 0.58402047
Axis point -1.76436098 0.00000000 -47.18208786
Rotation angle (degrees) 0.20134459
Shift along axis -0.05299829
> fitmap #11 inMap #2
Fit map J407_component_000_frame_015.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 183507 points
correlation = 0.9009, correlation about mean = 0.5877, overlap = 5090
steps = 48, shift = 0.208, angle = 0.483 degrees
Position of J407_component_000_frame_015.mrc z flip (#11) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999091 -0.00273836 0.00326767 0.05590994
0.00274708 0.99999267 -0.00266766 -0.12998441
-0.00326034 0.00267661 0.99999110 -0.02714748
Axis 0.53107566 0.64870698 0.54510357
Axis point 3.35863162 0.00000000 -28.38436861
Rotation angle (degrees) 0.28828800
Shift along axis -0.06942757
> fitmap #12 inMap #2
Fit map J407_component_000_frame_014.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 185464 points
correlation = 0.8578, correlation about mean = 0.4936, overlap = 4655
steps = 56, shift = 0.29, angle = 0.782 degrees
Position of J407_component_000_frame_014.mrc z flip (#12) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99997895 -0.00391909 0.00517094 0.00256972
0.00394209 0.99998236 -0.00444391 -0.08633596
-0.00515344 0.00446420 0.99997676 -0.05838787
Axis 0.56595594 0.65593568 0.49944195
Axis point -3.11241061 0.00000000 -9.74033626
Rotation angle (degrees) 0.45092040
Shift along axis -0.08433783
> fitmap #13 inMap #2
Fit map J407_component_000_frame_013.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 188095 points
correlation = 0.8116, correlation about mean = 0.4086, overlap = 4243
steps = 96, shift = 0.393, angle = 1.53 degrees
Position of J407_component_000_frame_013.mrc z flip (#13) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99992688 -0.00630498 0.01031927 -0.30501394
0.00639187 0.99994421 -0.00840964 0.04351622
-0.01026567 0.00847499 0.99991139 0.09565506
Axis 0.57242910 0.69787876 0.43045344
Axis point 13.43257006 0.00000000 23.93624556
Rotation angle (degrees) 0.84504164
Shift along axis -0.10305476
> fitmap #14 inMap #2
Fit map J407_component_000_frame_012.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 190432 points
correlation = 0.8261, correlation about mean = 0.4787, overlap = 4037
steps = 176, shift = 1.44, angle = 10.6 degrees
Position of J407_component_000_frame_012.mrc z flip (#14) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99694118 -0.00490893 0.07800121 -9.93956782
0.00881435 0.99872014 -0.04980352 5.90096487
-0.07765690 0.05033871 0.99570850 5.09045949
Axis 0.53956818 0.83868878 0.07394129
Axis point 58.43220848 0.00000000 129.45965602
Rotation angle (degrees) 5.32462315
Shift along axis -0.03760638
> fitmap #15 inMap #2
Fit map J407_component_000_frame_011.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 192986 points
correlation = 0.8264, correlation about mean = 0.5098, overlap = 4134
steps = 292, shift = 1.7, angle = 13.1 degrees
Position of J407_component_000_frame_011.mrc z flip (#15) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99535227 -0.00254091 0.09626734 -12.75691240
0.00845357 0.99809823 -0.06106117 7.73661469
-0.09592911 0.06159118 0.99348082 6.58346657
Axis 0.53732932 0.84199599 0.04816585
Axis point 59.44846482 0.00000000 135.25518533
Rotation angle (degrees) 6.55353132
Shift along axis -0.02336624
> fitmap #16 inMap #2
Fit map J407_component_000_frame_010.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 196011 points
correlation = 0.8258, correlation about mean = 0.5264, overlap = 4268
steps = 196, shift = 3.64, angle = 7.16 degrees
Position of J407_component_000_frame_010.mrc z flip (#16) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99443723 -0.00129423 0.10532294 -14.14446568
0.00834325 0.99775057 -0.06651460 8.62606466
-0.10499994 0.06702333 0.99221111 7.38173986
Axis 0.53560639 0.84358259 0.03865489
Axis point 60.11494959 0.00000000 137.40139033
Rotation angle (degrees) 7.16115140
Shift along axis -0.01372784
> fitmap #17 inMap #2
Fit map J407_component_000_frame_009.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 199261 points
correlation = 0.8232, correlation about mean = 0.5306, overlap = 4420
steps = 136, shift = 3.94, angle = 7.55 degrees
Position of J407_component_000_frame_009.mrc z flip (#17) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99383750 -0.00051591 0.11084568 -14.99048576
0.00835653 0.99749218 -0.07028168 9.22600775
-0.11053144 0.07077485 0.99134944 7.80629725
Axis 0.53705726 0.84286912 0.03378085
Axis point 59.78820314 0.00000000 138.50939775
Rotation angle (degrees) 7.54608177
Shift along axis -0.01072884
> fitmap #18 inMap #2
Fit map J407_component_000_frame_008.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 203831 points
correlation = 0.8153, correlation about mean = 0.52, overlap = 4559
steps = 2000, shift = 4.22, angle = 7.99 degrees
Position of J407_component_000_frame_008.mrc z flip (#18) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99311478 0.00036012 0.11714484 -15.91996779
0.00844044 0.99717627 -0.07462070 10.01782949
-0.11684093 0.07509567 0.99030745 8.49776599
Axis 0.53873766 0.84197168 0.02907615
Axis point 61.09163915 0.00000000 139.97400207
Rotation angle (degrees) 7.98715498
Shift along axis 0.10512492
> fitmap #19 inMap #2
Fit map J407_component_000_frame_007.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 209283 points
correlation = 0.8104, correlation about mean = 0.5166, overlap = 4743
steps = 2000, shift = 4.27, angle = 7.92 degrees
Position of J407_component_000_frame_007.mrc z flip (#19) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99298926 0.00085186 0.11820153 -16.25189613
0.00754817 0.99747619 -0.07059942 9.40986459
-0.11796335 0.07099668 0.99047671 9.37694002
Axis 0.51406917 0.85740414 0.02431115
Axis point 68.09691265 0.00000000 141.27730169
Rotation angle (degrees) 7.91598383
Shift along axis -0.05857770
> fitmap #20 inMap #2
Fit map J407_component_000_frame_006.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 215308 points
correlation = 0.803, correlation about mean = 0.509, overlap = 4911
steps = 2000, shift = 4.59, angle = 7.95 degrees
Position of J407_component_000_frame_006.mrc z flip (#20) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99338714 0.00062278 0.11481118 -15.65271922
0.00828418 0.99699005 -0.07708568 10.23612069
-0.11451362 0.07752704 0.99039194 7.15534657
Axis 0.55880756 0.82883495 0.02769014
Axis point 50.84212432 0.00000000 138.94807270
Rotation angle (degrees) 7.95189644
Shift along axis -0.06467064
> fitmap #21 inMap #2
Fit map J407_component_000_frame_005.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 221943 points
correlation = 0.7975, correlation about mean = 0.5036, overlap = 5120
steps = 2000, shift = 4.83, angle = 8.46 degrees
Position of J407_component_000_frame_005.mrc z flip (#21) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99245648 0.00133502 0.12259016 -16.74608631
0.00870219 0.99665134 -0.08130423 11.00789413
-0.12228819 0.08175771 0.98912147 8.37528140
Axis 0.55407863 0.83208786 0.02503340
Axis point 55.97483404 -0.00000000 140.45584472
Rotation angle (degrees) 8.46162297
Shift along axis 0.09054828
> fitmap #22 inMap #2
Fit map J407_component_000_frame_004.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 228675 points
correlation = 0.7942, correlation about mean = 0.505, overlap = 5345
steps = 128, shift = 4.86, angle = 8.35 degrees
Position of J407_component_000_frame_004.mrc z flip (#22) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99249124 0.00154071 0.12230601 -16.79973741
0.00809048 0.99690400 -0.07821101 10.55194435
-0.12204785 0.07861326 0.98940602 8.69406762
Axis 0.53998559 0.84137207 0.02255251
Axis point 58.99611311 0.00000000 140.99153578
Rotation angle (degrees) 8.34952877
Shift along axis 0.00256822
> fitmap #23 inMap #2
Fit map J407_component_000_frame_003.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 235349 points
correlation = 0.7882, correlation about mean = 0.5, overlap = 5547
steps = 212, shift = 4.98, angle = 8.42 degrees
Position of J407_component_000_frame_003.mrc z flip (#23) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99239157 0.00173360 0.12310956 -16.93547458
0.00807332 0.99683268 -0.07911654 10.70058751
-0.12285679 0.07950849 0.98923436 8.68387043
Axis 0.54184790 0.84019752 0.02165588
Axis point 58.31141283 -0.00000000 141.17775832
Rotation angle (degrees) 8.41685965
Shift along axis 0.00221262
> fitmap #24 inMap #2
Fit map J407_component_000_frame_002.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 242114 points
correlation = 0.7826, correlation about mean = 0.4956, overlap = 5752
steps = 208, shift = 5.08, angle = 8.48 degrees
Position of J407_component_000_frame_002.mrc z flip (#24) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99225263 0.00189051 0.12422215 -17.10140627
0.00804439 0.99680826 -0.07942660 10.75407774
-0.12397582 0.07981055 0.98907041 8.85014965
Axis 0.53987514 0.84148650 0.02086400
Axis point 58.92464501 0.00000000 141.34912975
Rotation angle (degrees) 8.48068000
Shift along axis 0.00143673
> fitmap #25 inMap #2
Fit map J407_component_000_frame_001.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 249113 points
correlation = 0.7772, correlation about mean = 0.4915, overlap = 5962
steps = 188, shift = 5.18, angle = 8.55 degrees
Position of J407_component_000_frame_001.mrc z flip (#25) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99214829 0.00207808 0.12504976 -17.23705108
0.00803389 0.99673797 -0.08030494 10.89836189
-0.12480873 0.08067904 0.98889518 8.86701028
Axis 0.54150720 0.84045738 0.02003374
Axis point 58.45205449 0.00000000 141.52577979
Rotation angle (degrees) 8.54837308
Shift along axis 0.00326072
> fitmap #26 inMap #2
Fit map J407_component_000_frame_000.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 256043 points
correlation = 0.7721, correlation about mean = 0.488, overlap = 6173
steps = 148, shift = 5.26, angle = 8.6 degrees
Position of J407_component_000_frame_000.mrc z flip (#26) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99206661 0.00217833 0.12569448 -17.33798987
0.00806440 0.99668776 -0.08092267 10.99552196
-0.12545442 0.08129433 0.98876308 8.89667575
Axis 0.54245968 0.83985122 0.01968325
Axis point 58.22890126 -0.00000000 141.63243770
Rotation angle (degrees) 8.59910356
Shift along axis 0.00455761
> color grey
> volume morph #2-26
Map positions are not the same, J407_component_000_frame_023.mrc z flip #3 and
J407_component_000_frame_024.mrc z flip #2. Use the "volume resample" command
to make a copy of one map with the same grid as the other map.
> volume resample #3-26 onGrid #2
Opened J407_component_000_frame_023.mrc z flip resampled as #1, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_022.mrc z flip resampled as #27, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_021.mrc z flip resampled as #28, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_020.mrc z flip resampled as #29, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_019.mrc z flip resampled as #30, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_018.mrc z flip resampled as #31, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_017.mrc z flip resampled as #32, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_016.mrc z flip resampled as #33, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_015.mrc z flip resampled as #34, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_014.mrc z flip resampled as #35, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_013.mrc z flip resampled as #36, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_012.mrc z flip resampled as #37, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_011.mrc z flip resampled as #38, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_010.mrc z flip resampled as #39, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_009.mrc z flip resampled as #40, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_008.mrc z flip resampled as #41, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_007.mrc z flip resampled as #42, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_006.mrc z flip resampled as #43, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_005.mrc z flip resampled as #44, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_004.mrc z flip resampled as #45, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_003.mrc z flip resampled as #46, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_002.mrc z flip resampled as #47, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_001.mrc z flip resampled as #48, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_000.mrc z flip resampled as #49, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
> close #3-26
> rename #2 id #500
> rename #1 id #2
> rename #500 id #1
> color grey
> volume morph #2-49
Opened morph as #3, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> hide #!1 models
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
Unsupported scale factor (0.000000) detected on Display1
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::setPen: Painter not active
QPainter::setBrush: Painter not active
QPainter::drawPoints: Painter not active
QPainter::end: Painter not active, aborted
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::setPen: Painter not active
QPainter::setBrush: Painter not active
QPainter::drawPoints: Painter not active
QPainter::end: Painter not active, aborted
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev29_PostPhenix.pdb" format pdb
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 25299 atom styles
23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected
> split #1
Split ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) into 9 models
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb D #1.4
---
Chain | Description
D | No description available
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb E #1.5
---
Chain | Description
E | No description available
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb F #1.6
---
Chain | Description
F | No description available
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb G #1.7
---
Chain | Description
G | No description available
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb H #1.8
---
Chain | Description
H | No description available
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb I #1.9
---
Chain | Description
I | No description available
> hide #!1.1 models
> hide #1.2 models
> hide #!1.3 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.6 models
> select /G:548
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/ylODC_54bp-
> oriC061_complete/cryosparc_P370_J327_even_better_Orc2WHD.mrc"
Opened cryosparc_P370_J327_even_better_Orc2WHD.mrc as #2, grid size
440,440,440, pixel 0.827, shown at level 0.0402, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1468
> select clear
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> vop flip #2
Opened cryosparc_P370_J327_even_better_Orc2WHD.mrc z flip as #3, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/ylODC_54bp-
> oriC061_complete/cryosparc_P370_J327_FLIPPED_even_better_Orc2WHD.mrc" models
> #3
Unsupported scale factor (0.000000) detected on Display1
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/ylODC_54bp-
> oriC061_complete/cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc"
Opened cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc as #4, grid
size 440,440,440, pixel 0.827, shown at level 0.0436, step 2, values float32
> select ~sel & ##selected
Nothing selected
> vop flip #4
Opened cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc z flip as #5,
grid size 440,440,440, pixel 0.827, shown at step 1, values float32
> close #4
> volume #5 level 0.1372
> volume #3 level 0.14
> volume #5 level 0.14
> volume #5 level 0.1
> volume #3 level 0.1
> volume #3 level 0.0813
> volume #3 level 0.1
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/ylODC_54bp-
> oriC061_complete/cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc"
Opened cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc as #4, grid size
440,440,440, pixel 0.827, shown at level 0.0683, step 2, values float32
> close #5
> vop flip #4
Opened cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc z flip as #5, grid
size 440,440,440, pixel 0.827, shown at step 1, values float32
> close #4
> volume #5 level 0.1
> volume #5 level 0.12
> volume #5 level 0.1
> volume #5 level 0.095
> volume #5 level 0.08
> hide #!3 models
> hide #!1 models
> surface dust #5 size 8.27
> close #5
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-
> Tor_Lab/test_a3d8f/test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #4
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select add #4
6005 atoms, 6077 bonds, 374 residues, 1 model selected
> ui mousemode right select
> select clear
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/test_a3d8f/1j7v-crystal
> structure.pdb"
1j7v-crystal structure.pdb title:
Human il-10 / il-10R1 complex [more info...]
Chain information for 1j7v-crystal structure.pdb #5
---
Chain | Description | UniProt
L | IL-10; cytokine synthesis inhibitory factor; CSIF | IL10_HUMAN 1-160
R | IL-10R1; IL-10R-A | I10R1_HUMAN 1-214
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #4 to #5
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1j7v-crystal structure.pdb, chain R (#5) with
test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb, chain
B (#4), sequence alignment score = 1073
RMSD between 192 pruned atom pairs is 0.747 angstroms; (across all 205 pairs:
1.150)
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-
> Tor_Lab/test_a3d8f/test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #6
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select ~sel & ##selected
Nothing selected
> matchmaker #6 to #5
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1j7v-crystal structure.pdb, chain R (#5) with
test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain
B (#6), sequence alignment score = 1073
RMSD between 191 pruned atom pairs is 0.713 angstroms; (across all 205 pairs:
1.091)
> close #4
> close #6
> ui tool show "Unit Cell"
> unitcell #5
> unitcell delete #5
> unitcell #5
Drag select of 587 residues
> delete sel
Drag select of 832 residues, 8 pseudobonds
> delete sel
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-
> Tor_Lab/test_a3d8f/test_566b6.result.zip
Unrecognized file suffix '.zip'
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-
> Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb #6
---
Chain | Description
A B | No description available
C D | No description available
Computing secondary structure
> hide #!4 models
> show #!4 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #!4 models
> close #5
> matchmaker #6 to #4
Specify a single 'to' model only
> hide #4.1 models
> show #4.1 models
> hide #4.2 models
> show #4.2 models
> hide #!4.3 models
> show #!4.3 models
> hide #4.4 models
> show #4.4 models
> close #4
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/test_a3d8f/1j7v-crystal
> structure.pdb" format pdb
1j7v-crystal structure.pdb title:
Human il-10 / il-10R1 complex [more info...]
Chain information for 1j7v-crystal structure.pdb #4
---
Chain | Description | UniProt
L | IL-10; cytokine synthesis inhibitory factor; CSIF | IL10_HUMAN 1-160
R | IL-10R1; IL-10R-A | I10R1_HUMAN 1-214
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> unitcell #4
> combine #5
Remapping chain ID 'L' in 1j7v-crystal structure.pdb #2 #5.2 to 'M'
Remapping chain ID 'R' in 1j7v-crystal structure.pdb #2 #5.2 to 'S'
Remapping chain ID 'L' in 1j7v-crystal structure.pdb #3 #5.3 to 'N'
Remapping chain ID 'R' in 1j7v-crystal structure.pdb #3 #5.3 to 'T'
Remapping chain ID 'L' in 1j7v-crystal structure.pdb #4 #5.4 to 'O'
Remapping chain ID 'R' in 1j7v-crystal structure.pdb #4 #5.4 to 'U'
Remapping chain ID 'L' in 1j7v-crystal structure.pdb #5 #5.5 to 'P'
Remapping chain ID 'R' in 1j7v-crystal structure.pdb #5 #5.5 to 'V'
Remapping chain ID 'L' in 1j7v-crystal structure.pdb #6 #5.6 to 'Q'
Remapping chain ID 'R' in 1j7v-crystal structure.pdb #6 #5.6 to 'W'
> hide #4 models
> hide #!5 models
> matchmaker #6 to #7
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain R (#7) with
test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb, chain
C (#6), sequence alignment score = 1073
RMSD between 194 pruned atom pairs is 0.648 angstroms; (across all 205 pairs:
1.044)
> select add #6
12010 atoms, 12154 bonds, 748 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.51645,0.16079,-0.84109,16.615,-0.7222,0.60956,-0.32692,27.053,0.46012,0.77627,0.43093,122.67
> matchmaker #6 to #7
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain R (#7) with
test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb, chain
C (#6), sequence alignment score = 1073
RMSD between 194 pruned atom pairs is 0.648 angstroms; (across all 205 pairs:
1.044)
> view matrix models
> #6,0.51645,0.16079,-0.84109,16.006,-0.7222,0.60956,-0.32692,15.467,0.46012,0.77627,0.43093,137.76
> view matrix models
> #6,0.51645,0.16079,-0.84109,12.455,-0.7222,0.60956,-0.32692,-15.933,0.46012,0.77627,0.43093,154.19
> view matrix models
> #6,0.51645,0.16079,-0.84109,7.4024,-0.7222,0.60956,-0.32692,10.581,0.46012,0.77627,0.43093,164.48
> view matrix models
> #6,0.51645,0.16079,-0.84109,77.402,-0.7222,0.60956,-0.32692,32.484,0.46012,0.77627,0.43093,91.425
> close #6
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-
> Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb #6
---
Chain | Description
A B | No description available
C D | No description available
Computing secondary structure
> matchmaker #6 to #7
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain R (#7) with
test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb, chain
C (#6), sequence alignment score = 1052
RMSD between 190 pruned atom pairs is 0.752 angstroms; (across all 205 pairs:
1.415)
> close #6
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-
> Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #6
---
Chain | Description
A B | No description available
C D | No description available
Computing secondary structure
> matchmaker #6 to #7
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain R (#7) with
test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb, chain
D (#6), sequence alignment score = 1073
RMSD between 196 pruned atom pairs is 0.731 angstroms; (across all 205 pairs:
1.005)
> close #6
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-
> Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb #6
---
Chain | Description
A B | No description available
C D | No description available
Computing secondary structure
> matchmaker #6 to #7
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain R (#7) with
test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb, chain
C (#6), sequence alignment score = 1073
RMSD between 193 pruned atom pairs is 0.707 angstroms; (across all 205 pairs:
1.082)
> close #6
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-
> Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb #6
---
Chain | Description
A B | No description available
C D | No description available
Computing secondary structure
> matchmaker #6 to #7
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain R (#7) with
test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb, chain
C (#6), sequence alignment score = 1073
RMSD between 192 pruned atom pairs is 0.722 angstroms; (across all 205 pairs:
1.163)
> close #6
> close #7
> close #5
> close #4
> close #1
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev29_PostPhenix.pdb"
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 25299 atom styles
23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected
> hide #!1 models
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb
7jk3-dmODC_GCrich.pdb title:
Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...]
Chain information for 7jk3-dmODC_GCrich.pdb #2
---
Chain | Description | UniProt
A | DMORC1 | ORC1_DROME 440-924
B | DMORC2 | ORC2_DROME 1-618
C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721
D | ORC4 | Q9W102_DROME 1-459
E | ORC5 | ORC5_DROME 1-460
F | ORC6 | ORC6_DROME 1-257
G | CDC6 | Q9VSM9_DROME 242-662
H | DNA (33-mer) |
I | DNA (33-mer) |
Non-standard residues in 7jk3-dmODC_GCrich.pdb #2
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
> close #2
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/hsORC1-6_CDC6_60bpDNA.pdb
Chain information for hsORC1-6_CDC6_60bpDNA.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 46715 atom styles
43798 atoms, 44629 bonds, 22 pseudobonds, 5455 residues, 4 models selected
Computing secondary structure
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7mca-assembly1.cif
7mca-assembly1.cif title:
Structure of the S. cerevisiae origin recognition complex bound to the
replication initiator Cdc6 and the ARS1 origin DNA. [more info...]
Chain information for 7mca-assembly1.cif #3
---
Chain | Description
A | Origin recognition complex subunit 1
B | Origin recognition complex subunit 2
C | Origin recognition complex subunit 3
D | Origin recognition complex subunit 4
E | Origin recognition complex subunit 5
F | Origin recognition complex subunit 6
G | DNA (85-MER)
H | DNA (85-MER)
I | Cell division control protein 6
Non-standard residues in 7mca-assembly1.cif #3
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> modelfix
Changed 71407 atom styles
66312 atoms, 67574 bonds, 36 pseudobonds, 8215 residues, 6 models selected
> newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H
> select #1/H,I
1476 atoms, 1654 bonds, 72 residues, 1 model selected
> show #!1 models
> ui mousemode right select
> select clear
> matchmaker #2,3 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1
RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
7.882)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 943
RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
5.169)
> matchmaker #2,3 to #1/C:180-260,/D,/E
Invalid "to" argument: only initial part "#1/C:180-260" of atom specifier
valid
> matchmaker #2,3 to (#1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain E (#2), sequence alignment score = 281.2
RMSD between 99 pruned atom pairs is 0.965 angstroms; (across all 120 pairs:
3.490)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca-
assembly1.cif, chain E (#3), sequence alignment score = 312.4
RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
3.466)
> matchmaker #2,3 to (#1/A:300-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 836.2
RMSD between 200 pruned atom pairs is 1.167 angstroms; (across all 283 pairs:
2.305)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 700.3
RMSD between 218 pruned atom pairs is 0.943 angstroms; (across all 276 pairs:
5.480)
> matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4
RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
2.238)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 527.5
RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
2.175)
> matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5
RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs:
2.171)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca-
assembly1.cif, chain E (#3), sequence alignment score = 312.4
RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
3.466)
> matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4
RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
2.238)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 527.5
RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
2.175)
> select ~nucleic
66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected
> show sel surfaces
> transparency 30 surfaces
> transparency 70 surfaces
> hide sel cartoons
> matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5
RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs:
2.171)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca-
assembly1.cif, chain E (#3), sequence alignment score = 312.4
RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
3.466)
> matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4
RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
2.238)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 527.5
RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
2.175)
> matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4
RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
2.238)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 527.5
RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
2.175)
> matchmaker #2,3 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1
RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
7.882)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 943
RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
5.169)
Drag select of ylODC_54bpOriC061_rev29_PostPhenix.pdb_A SES surface, 7 of
358676 triangles, ylODC_54bpOriC061_rev29_PostPhenix.pdb_D SES surface, 18 of
396086 triangles, hsORC1-6_CDC6_60bpDNA.pdb_D SES surface, 38 of 440036
triangles
> select #2/A:901@C5'
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
3061 atoms, 3113 bonds, 385 residues, 1 model selected
> select down
31 atoms, 33 bonds, 1 residue, 2 models selected
> select clear
> matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5
RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs:
2.171)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca-
assembly1.cif, chain E (#3), sequence alignment score = 312.4
RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
3.466)
> matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4
RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
2.238)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 527.5
RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
2.175)
> matchmaker #2,3 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1
RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
7.882)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 943
RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
5.169)
> matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4
RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
2.238)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 527.5
RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
2.175)
> select #2
21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> show sel atoms
> undo
> show sel cartoons
> select clear
> matchmaker #2,3 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1
RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
7.882)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 943
RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
5.169)
> matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4
RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
2.238)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 527.5
RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
2.175)
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> hide sel surfaces
> select clear
> matchmaker #2,3 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1
RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
7.882)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 943
RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
5.169)
> matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4
RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
2.238)
Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 527.5
RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
2.175)
> select add #2
21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> select ~nucleic
66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected
> show sel surfaces
> select clear
> select ~nucleic
66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected
> hide sel cartoons
> hide sel atoms
> select clear
> color #1 FFFF80
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1 #FFFF80
> color #1 #FF8080
> color #2 #8080FF
> color #2 #0080FF
> color #3 #0080FF
> color #3 lime
> lighting full
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting full
> transparency 75 surfaces
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> nucleotides atoms
> style nucleic stick
Changed 4715 atom styles
> nucleotides fill
> style nucleic stick
Changed 4715 atom styles
> nucleotides tube/slab shape box
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> lighting soft
> hide #!2 models
> hide #!1 models
> | #3/I) /Z /Z
Expected fewer arguments
>
Missing or invalid eighth argument: Expected a text string
> newcolor /A /B /C /D /E /F #1/G /Z /Z
> newcolor /A /B /C /D /E /F #2/G /Z /Z
> newcolor /A /B /C /D /E /F #3/I /Z /Z
> transparency 75 surfaces
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> color #3 #0080FF
> color #2 lime
> newcolor /A /B /C /D /E /F #3/I /Z /Z
> newcolor /A /B /C /D /E /F #2/G /Z /Z
> transparency 75 surfaces
> hide #!3 models
> hide #!2 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/ylODC_54oriC_bend_updated.png" supersample 3
> show #!2 models
> hide #!1 models
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/hsODC_bend_updated.png" supersample 3
> show #!3 models
> hide #!2 models
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/scODC_bend_updated.png" supersample 3
> show #!1 models
> show #!2 models
> transparency 50 surfaces
> hide #!2 models
> hide #!3 models
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/ylODC_54oriC_bend_updated2.png" supersample 3
> show #!2 models
> hide #!1 models
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/hsODC_bend_updated2.png" supersample 3
> hide #!2 models
> show #!3 models
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/scODC_bend_updated2.png" supersample 3
> ui tool show "Side View"
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> lighting full
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1-2 cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> close #2-3
> hide surfaces
> select /A,B,C,E,F
16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected
> hide sel cartoons
> select /D:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G:557
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G:548
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> lighting shadows false
> modelfix
Changed 25299 atom styles
23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected
> select /A,B,C,E,F
16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected
> hide sel cartoons
> select clear
> select /D:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G:560
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /G:557
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G:548
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> nucleotides tube/slab shape box
> nucleotides fill
> style nucleic stick
Changed 1476 atom styles
> nucleotides fill
> style nucleic stick
Changed 1476 atom styles
> nucleotides ladder
> nucleotides fill
> style nucleic stick
Changed 1476 atom styles
> nucleotides fill
> style nucleic stick
Changed 1476 atom styles
> nucleotides atoms
> style nucleic stick
Changed 1476 atom styles
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/Orc4-Cdc6-element-54bpOriC061-ver1.png" supersample 3
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb"
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 50598 atom styles
47398 atoms, 48290 bonds, 18 pseudobonds, 5940 residues, 4 models selected
> select /A,B,C,E,F
33274 atoms, 33942 bonds, 8 pseudobonds, 4146 residues, 6 models selected
> hide sel cartoons
> select ~nucleic
47646 atoms, 48546 bonds, 22 pseudobonds, 5956 residues, 6 models selected
> hide sel atoms
> select clear
Drag select of 10 residues
> select clear
Drag select of 2 residues
> show sel atoms
> select #2/D:465@NZ
1 atom, 1 residue, 1 model selected
> ui tool show "Add Hydrogens"
> addh #!2
Summary of feedback from adding hydrogens to
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2
---
warnings | Not adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/H DG 8 P because it is missing heavy-atom bond partners
Not adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 13 P
because it is missing heavy-atom bond partners
notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain A determined from SEQRES records
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain B determined
from SEQRES records
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
C; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
D; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
E; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
F; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
G; guessing termini instead
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain H determined
from SEQRES records
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain I determined
from SEQRES records
Chain-initial residues that are actual N termini:
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/A PRO 299,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/B PRO 106,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C THR 6,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D VAL 34,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 1,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F PRO 179,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G PRO 93,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C THR 6,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D VAL 34,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 1,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F PRO 179,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F GLY 316,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G PRO 93,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ALA 213,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G THR 386,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G VAL 439
Chain-initial residues that are not actual N termini:
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F GLY 316,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ALA 213,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G THR 386,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G VAL 439
Chain-final residues that are actual C termini:
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/A LEU 718,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/B LEU 507,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C LEU 685,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D ARG 511,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ARG 29,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C LEU 685,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D SER 123,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D MET 285,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 420,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D ARG 511,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 300,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASN 464,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F THR 307,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F LYS 349,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G GLY 207,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G HIS 335,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ASN 434,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G LYS 602
Chain-final residues that are not actual C termini:
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ARG 29,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D SER 123,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D MET 285,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 420,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASN 464,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 300,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F LYS 349,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F THR 307,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G LYS 602,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G GLY 207,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G HIS 335,
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ASN 434
Chain-initial residues that are not actual 5' termini:
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 13
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
#2/B LEU 507
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
#2/C ARG 29
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
#2/D SER 123
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
#2/D MET 285
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
#2/D LEU 420
8 messages similar to the above omitted
3052 hydrogen bonds
Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72
Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127
Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296
Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436
Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319
4 messages similar to the above omitted
24712 hydrogens added
> select #1/D:465@CE
1 atom, 1 residue, 1 model selected
> ui tool show "Add Hydrogens"
> addh #!1
Summary of feedback from adding hydrogens to
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1
---
warnings | Not adding hydrogens to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/H DG 8 P because it is missing heavy-atom bond partners
Not adding hydrogens to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 13 P
because it is missing heavy-atom bond partners
notes | Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain A determined from SEQRES records
Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain B determined
from SEQRES records
No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
C; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
D; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
E; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
F; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
G; guessing termini instead
Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain H determined
from SEQRES records
Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain I determined
from SEQRES records
Chain-initial residues that are actual N termini:
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/A PRO 299,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/B PRO 106,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C THR 6,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D VAL 34,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 1,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F PRO 179,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G PRO 93,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C THR 6,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D VAL 34,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 1,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F PRO 179,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F GLY 316,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G PRO 93,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ALA 213,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G THR 386,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G VAL 439
Chain-initial residues that are not actual N termini:
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F GLY 316,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ALA 213,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G THR 386,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G VAL 439
Chain-final residues that are actual C termini:
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/A LEU 718,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/B LEU 507,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C LEU 685,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D ARG 511,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ARG 29,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C LEU 685,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D SER 123,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D MET 285,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 420,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D ARG 511,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 300,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASN 464,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F THR 307,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F LYS 349,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G GLY 207,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G HIS 335,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ASN 434,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G LYS 602
Chain-final residues that are not actual C termini:
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ARG 29,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D SER 123,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D MET 285,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 420,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASN 464,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 300,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F LYS 349,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F THR 307,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G LYS 602,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G GLY 207,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G HIS 335,
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ASN 434
Chain-initial residues that are not actual 5' termini:
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 13
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
#1/B LEU 507
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
#1/C ARG 29
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
#1/D SER 123
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
#1/D MET 285
Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
#1/D LEU 420
8 messages similar to the above omitted
3042 hydrogen bonds
Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72
Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127
Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296
Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436
Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319
4 messages similar to the above omitted
24712 hydrogens added
> ui tool show H-Bonds
> select #1/D:465
22 atoms, 21 bonds, 1 residue, 1 model selected
> hbonds sel restrict #1/H,I twoColors true intraRes false reveal true log
> true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 ylODC_54bpOriC061_rev29_PostPhenix.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 NZ ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 31 O6 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 HZ1 2.845 1.875
ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 NZ ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 32 N7 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 HZ2 3.459 2.599
2 hydrogen bonds found
0 strict hydrogen bonds found
> select #2/D:465
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict #2/H,I twoColors true intraRes false reveal true log
> true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 ylODC_54bpOriC061_rev30_PostPhenix.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 NZ ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 31 O6 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 HZ1 2.363 1.498
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 NZ ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 32 O6 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 HZ2 2.546 1.684
2 hydrogen bonds found
0 strict hydrogen bonds found
> ui tool show "Side View"
> close #2
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb" format pdb
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 75323 atom styles
71260 atoms, 72152 bonds, 18 pseudobonds, 5940 residues, 4 models selected
> close #1
> select /A,B,C,E,F
16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected
> hide sel cartoons
> select clear
> select ~nucleic
23823 atoms, 24273 bonds, 11 pseudobonds, 2978 residues, 3 models selected
> hide sel atoms
> select clear
> select /D:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G:548
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G:557
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/Orc4-Cdc6-element-54bpOriC061-ver1.png" supersample 3
> select clear
> select /A,B,C,E,F
16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected
> show sel atoms
> undo
> show sel cartoons
> color sel #808080
> color sel #AAAAAA
> color sel #BBBBBB
> transparency 70 r
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 70 cartoons
> select clear
> undo
> transparency 0 ribbons
> transparency 0 r
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 0 sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency sel 70 target c
> transparency sel 90 target c
> transparency sel 80 target c
> transparency sel 75 target c
> select clear
> select /A,B,C,E,F
16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected
> hide sel cartoons
> show sel cartoons
> select clear
> turn x 2 180
> wait 180
> turn y 2 180
> wait 180
> turn y 2 180
> wait 180
> select /A,B,C,E,F
16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected
> hide sel cartoons
> select up
25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected
> select up
25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected
> select clear
> turn y 2 180
> wait 180
> turn y 2 180
> wait 180
> turn y 2 180
> wait 180
> turn y 2 180
> wait 180
> turn y 2 180
> wait 180
> select /I:32@O6
1 atom, 1 residue, 1 model selected
> turn y 2 180 centerOn sel ; wait 180
Expected a keyword
> turn y 2 180 centerOn sel ; wait 180
Expected a keyword
> turn y 2 180 center sel
> wait 180
> select clear
> turn y 2 180 center sel ; wait 180
Invalid "center" argument: Center argument no objects specified
> select /I:31@O6
1 atom, 1 residue, 1 model selected
> turn y 2 180 center sel
> wait 180
> turn y 2 180 center (#1/I:31 | #1/H:24) ; wait 180
Invalid "center" argument: Center argument no objects specified
> select clear
> turn y 2 180 center (#1/I:31 | #1/H:24) ; wait 180
Invalid "center" argument: Center argument no objects specified
> turn y 2 180 center #1/I:31 ; wait 180
Invalid "center" argument: Center argument no objects specified
> turn y 2 180 models #1/I:31
> wait 180
> turn y 2 180 models #1/I:31
> wait 180
> turn y 2 180 models #1/I:31
> turn y 2 180 models #1 center #1/I:31
Invalid "center" argument: Center argument no objects specified
> select clear
> select /I:31@O6
1 atom, 1 residue, 1 model selected
> select clear
> turn y 2 180 models #1 center #1/I:31@O6
Invalid "center" argument: Center argument no objects specified
> turn y 2 180 center #1/I:31@O6
Invalid "center" argument: Center argument no objects specified
> select /I:31@O6
1 atom, 1 residue, 1 model selected
> turn y 2 180 center /I:31@O6
> select clear
> turn y 2 180 center /I:31@O6
> turn y 1 360 center /I:31@O6
> wait 360
> turn y 1 360 center /I:31@O6
> wait 360
> movie record supersample 3
> turn y 2 180 center /I:31@O6
> wait 180
> movie encode "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/Orc4-Cdc6-binding-region-54bpOriC.mp4"
Movie saved to /Users/jtbauer/.../figures for posterpub/Orc4-Cdc6-binding-
region-54bpOriC.mp4
> turn y 2 180 center /I:31@O6
> wait 180
> turn y 2 180 center /I:31@O6
> wait 180
> turn y 2 180 center /I:31@O6
> wait 180
> turn y 2 180 center /I:31@O6
> wait 180
> turn y 2 180 center /I:31@O6
> wait 180
> turn y 2 180 center /I:31@O6
> wait 180
> turn y 2 180 center /I:31@O6
> wait 180
> turn y 2 180 center /I:31@O6
> wait 180
> turn y 2 180 center /I:31@O6
> wait 180
> movie record supersample 3
> turn y 2 180 center /I:31@O6
> wait 180
> movie encode "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/Orc4-Cdc6-binding-region-54bpOriC-camera2.mp4"
Movie saved to /Users/jtbauer/.../figures for posterpub/Orc4-Cdc6-binding-
region-54bpOriC-camera2.mp4
> show cartoons
> transparency 0 cartoons
> modelfix
Changed 25299 atom styles
23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected
> select nucleic
1476 atoms, 1654 bonds, 72 residues, 1 model selected
> ui tool show "Add Hydrogens"
> addh #!2
Summary of feedback from adding hydrogens to
ylODC_54bpOriC061_rev30_PostPhenix.pdb #2
---
warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners
Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond
partners
notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain A determined from SEQRES records
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain B determined
from SEQRES records
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
C; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
D; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
E; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
F; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
G; guessing termini instead
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain H determined
from SEQRES records
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain I determined
from SEQRES records
Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C
THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL
34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F
GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439
Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127,
/D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL
439
Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU
685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D
ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS
335, /G ASN 434, /G LYS 602
Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D
MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS
602, /G GLY 207, /G HIS 335, /G ASN 434
Chain-initial residues that are not actual 5' termini: /I DG 13
Missing OXT added to C-terminal residue /B LEU 507
Missing OXT added to C-terminal residue /C ARG 29
Missing OXT added to C-terminal residue /D SER 123
Missing OXT added to C-terminal residue /D MET 285
Missing OXT added to C-terminal residue /D LEU 420
8 messages similar to the above omitted
3052 hydrogen bonds
Adding 'H' to /C ASN 72
Adding 'H' to /D GLN 127
Adding 'H' to /D LEU 296
Adding 'H' to /D PHE 436
Adding 'H' to /E ASP 319
4 messages similar to the above omitted
24712 hydrogens added
> ui tool show H-Bonds
> hbonds sel restrict #2/A,B,C,D,E,F,G twoColors true intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 ylODC_54bpOriC061_rev30_PostPhenix.pdb
61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
61 hydrogen bonds found
21 strict hydrogen bonds found
> split #2
Split ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) into 9 models
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb C #2.3
---
Chain | Description
C | No description available
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb D #2.4
---
Chain | Description
D | No description available
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb E #2.5
---
Chain | Description
E | No description available
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb F #2.6
---
Chain | Description
F | No description available
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb G #2.7
---
Chain | Description
G | No description available
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb H #2.8
---
Chain | Description
H | No description available
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb I #2.9
---
Chain | Description
I | No description available
> select add #2.8
1170 atoms, 1262 bonds, 37 residues, 1 model selected
> select add #2.9
2291 atoms, 2469 bonds, 72 residues, 2 models selected
> hbonds sel restrict #2/A,B,C,D,E,F,G twoColors true intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2.7 ylODC_54bpOriC061_rev30_PostPhenix.pdb G
2.9 ylODC_54bpOriC061_rev30_PostPhenix.pdb I
2.8 ylODC_54bpOriC061_rev30_PostPhenix.pdb H
2.1 ylODC_54bpOriC061_rev30_PostPhenix.pdb A
2.2 ylODC_54bpOriC061_rev30_PostPhenix.pdb B
2.3 ylODC_54bpOriC061_rev30_PostPhenix.pdb C
2.4 ylODC_54bpOriC061_rev30_PostPhenix.pdb D
2.5 ylODC_54bpOriC061_rev30_PostPhenix.pdb E
2.6 ylODC_54bpOriC061_rev30_PostPhenix.pdb F
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> close #2
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb" format pdb
Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 25299 atom styles
23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected
> select nucleic
1476 atoms, 1654 bonds, 72 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2" restrict
> #2/A,B,C,D,E,F,G twoColors true intraRes false reveal true log true
'restrict' atom specifier selects no atoms
> ui tool show "Add Hydrogens"
> addh #!1
Summary of feedback from adding hydrogens to
ylODC_54bpOriC061_rev30_PostPhenix.pdb #1
---
warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners
Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond
partners
notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain A determined from SEQRES records
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain B determined
from SEQRES records
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
C; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
D; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
E; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
F; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
G; guessing termini instead
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain H determined
from SEQRES records
Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain I determined
from SEQRES records
Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C
THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL
34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F
GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439
Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127,
/D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL
439
Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU
685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D
ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS
335, /G ASN 434, /G LYS 602
Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D
MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS
602, /G GLY 207, /G HIS 335, /G ASN 434
Chain-initial residues that are not actual 5' termini: /I DG 13
Missing OXT added to C-terminal residue /B LEU 507
Missing OXT added to C-terminal residue /C ARG 29
Missing OXT added to C-terminal residue /D SER 123
Missing OXT added to C-terminal residue /D MET 285
Missing OXT added to C-terminal residue /D LEU 420
8 messages similar to the above omitted
3052 hydrogen bonds
Adding 'H' to /C ASN 72
Adding 'H' to /D GLN 127
Adding 'H' to /D LEU 296
Adding 'H' to /D PHE 436
Adding 'H' to /E ASP 319
4 messages similar to the above omitted
24712 hydrogens added
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2" restrict
> #1/A,B,C,D,E,F,G twoColors true intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
61 hydrogen bonds found
21 strict hydrogen bonds found
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
> restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
> reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
74 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236
/G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601
/G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
74 hydrogen bonds found
21 strict hydrogen bonds found
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
> restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
> select true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
74 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236
/G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601
/G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
74 hydrogen bonds found
21 strict hydrogen bonds found
> select up
1950 atoms, 1998 bonds, 79 residues, 1 model selected
> show sel atoms
> select clear
> select ~nucleic
47733 atoms, 48183 bonds, 11 pseudobonds, 2978 residues, 3 models selected
> hide sel cartoons
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"
> select /G:548@NZ
1 atom, 1 residue, 1 model selected
> select /I:29@N3
1 atom, 1 residue, 1 model selected
> select /I:30
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /I:29
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /H:26
32 atoms, 34 bonds, 1 residue, 1 model selected
> ui tool show "Renumber Residues"
> renumber /H start -7
37 residues renumbered
> select /H:12
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /H:11
32 atoms, 34 bonds, 1 residue, 1 model selected
> renumber /H start -16
37 residues renumbered
> renumber /H start -16
0 residues renumbered
> renumber /H start -16
0 residues renumbered
> select /H:3
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /H:2
32 atoms, 34 bonds, 1 residue, 1 model selected
> renumber /H start -18
37 residues renumbered
> select /H:0
32 atoms, 34 bonds, 1 residue, 1 model selected
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"
> select /I:29
32 atoms, 33 bonds, 1 residue, 1 model selected
> ui tool show "Renumber Residues"
> renumber /I start -15
35 residues renumbered
> select /I:1
32 atoms, 33 bonds, 1 residue, 1 model selected
> renumber /I start -16
35 residues renumbered
> renumber /I start -16
0 residues renumbered
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30" restrict
> #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false select true
> reveal true log true
Atom specifier selects no atoms
> select nucleic
2291 atoms, 2469 bonds, 72 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
> restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
> select true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
74 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 18 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT -16 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC -15 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 17 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 18 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC -13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA -12 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC -13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC -13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG -10 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 9 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG -10 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 9 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 8 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 8 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 10 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 10 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT -8 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 12 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 11 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DA -11 N3 /C ARG 220 HH12 3.522 2.929
/C ARG 220 NH1 /H DT -10 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 11 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA -9 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 6 OP2 /C TYR 607 HH 3.278 2.327
/C LYS 671 N /H DC 6 OP1 /C LYS 671 H 2.864 2.159
/C ARG 672 N /H DC 6 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT -4 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT -4 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 7 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA -12 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA -12 O3' /D SER 169 HG 3.382 2.801
/D SER 169 OG /H DA -11 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA -11 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 1 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 2 N7 /D LYS 465 HZ1 3.444 2.853
/D LYS 465 NZ /I DG 2 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 3 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA -9 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG -10 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG -10 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG -10 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC -9 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /I DT -13 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT -13 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT -13 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 15 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG -10 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG -10 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT -11 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG -10 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 12 O2 /E ARG 362 HH22 2.881 2.130
/E ARG 362 NH2 /H DA 13 O4' /E ARG 362 HH21 3.366 2.779
/E LYS 363 N /I DC -9 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA -8 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 543 N /H DA 0 OP1 /G GLY 543 H 2.943 2.343
/G GLY 546 N /H DA 1 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 2 O3' /G LYS 547 HZ2 2.870 2.326
/G LYS 547 NZ /I DG 3 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /H DA 1 N3 /G LYS 548 HZ1 2.902 2.236
/G LYS 548 NZ /H DG 2 O4' /G LYS 548 HZ2 2.987 2.212
/G LYS 548 NZ /I DT 0 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 3 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 5 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 5 N7 /G ARG 557 HH22 2.372 1.443
/G LYS 560 NZ /H DA -11 OP1 /G LYS 560 HZ3 3.180 2.601
/G GLY 561 N /H DT -10 OP1 /G GLY 561 H 3.390 2.598
/G GLY 561 N /H DT -10 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 N /H DT -10 OP1 /G THR 563 H 2.931 2.306
/G THR 563 OG1 /H DT -10 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA -9 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 3 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 0 O5' /G LYS 581 HZ1 3.367 2.792
/G LYS 581 NZ /H DA 0 OP2 /G LYS 581 HZ1 3.143 2.140
74 hydrogen bonds found
21 strict hydrogen bonds found
> show sel atoms
> select clear
> ui tool show "Change Chain IDs"
> changechains H main
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (main/299/)
> changechains H main
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (main/299/)
> changechains I opp
No residues specified
> changechains I opp
No residues specified
> changechains H main
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (main/299/)
> select /H
1170 atoms, 1262 bonds, 37 residues, 1 model selected
> changechains sel main
Chain IDs of 37 residues changed
> select /I
1121 atoms, 1207 bonds, 35 residues, 1 model selected
> changechains sel opp
Chain IDs of 35 residues changed
> select clear
> ui tool show H-Bonds
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
> restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
> reveal true log true
Atom specifier selects no atoms
> select nucleic
2291 atoms, 2469 bonds, 72 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
> restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
> reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
74 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /opp DC 18 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /main DT -16 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /main DC -15 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /opp DT 17 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /opp DC 18 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /main DC -13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /main DA -12 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /main DC -13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /main DC -13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /opp DG -10 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /main DG 9 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /opp DG -10 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /main DG 9 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /main DT 8 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /opp DA 8 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /opp DA 10 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /main DT -8 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /opp DT 12 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /opp DT 11 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /main DA -11 N3 /C ARG 220 HH12 3.522 2.929
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /main DA -9 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.278 2.327
/C LYS 671 N /main DC 6 OP1 /C LYS 671 H 2.864 2.159
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /main DA 7 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /main DA -12 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /main DA -12 O3' /D SER 169 HG 3.382 2.801
/D SER 169 OG /main DA -11 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /main DA -11 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /opp DG 1 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.444 2.853
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /main DA -9 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /opp DG -10 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /opp DG -10 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /opp DG -10 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /opp DC -9 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /opp DT -13 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /opp DG -10 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /opp DG -10 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /opp DT -11 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /opp DG -10 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /main DT 12 O2 /E ARG 362 HH22 2.881 2.130
/E ARG 362 NH2 /main DA 13 O4' /E ARG 362 HH21 3.366 2.779
/E LYS 363 N /opp DC -9 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /opp DA -8 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 543 N /main DA 0 OP1 /G GLY 543 H 2.943 2.343
/G GLY 546 N /main DA 1 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /opp DG 2 O3' /G LYS 547 HZ2 2.870 2.326
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /main DA 1 N3 /G LYS 548 HZ1 2.902 2.236
/G LYS 548 NZ /main DG 2 O4' /G LYS 548 HZ2 2.987 2.212
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /opp DG 5 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /opp DG 5 N7 /G ARG 557 HH22 2.372 1.443
/G LYS 560 NZ /main DA -11 OP1 /G LYS 560 HZ3 3.180 2.601
/G GLY 561 N /main DT -10 OP1 /G GLY 561 H 3.390 2.598
/G GLY 561 N /main DT -10 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 N /main DT -10 OP1 /G THR 563 H 2.931 2.306
/G THR 563 OG1 /main DT -10 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /main DA -9 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /opp DG 3 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /main DA 0 O5' /G LYS 581 HZ1 3.367 2.792
/G LYS 581 NZ /main DA 0 OP2 /G LYS 581 HZ1 3.143 2.140
74 hydrogen bonds found
21 strict hydrogen bonds found
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"
> select /main:-13
30 atoms, 31 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /A:436@ND2
1 atom, 1 residue, 1 model selected
> select /main:-12
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /main:-10
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /main:-11
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /main:-10
32 atoms, 33 bonds, 1 residue, 1 model selected
> select clear
> select /main:-9
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /main:-9
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /main:-8
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /main:-9
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select /main:-8
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /main:-9@C3'
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
32 atoms, 34 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select /main:0
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /main:0
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /main:1
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /main:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select nucleic
2291 atoms, 2469 bonds, 72 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2" dashes 6
> restrict #1/A,B,C,D,E,F,G twoColors true intraRes false reveal true
> retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /opp DC 18 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /main DT -16 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /main DC -15 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /opp DT 17 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /opp DC 18 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /main DC -13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /main DA -12 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /main DC -13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /main DC -13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /opp DG -10 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /main DG 9 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /opp DG -10 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /main DG 9 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /main DT 8 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /opp DA 8 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /opp DA 10 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /main DT -8 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /opp DT 12 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /opp DT 11 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /main DA -9 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.278 2.327
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /main DA 7 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /main DA -12 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /main DA -11 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /main DA -11 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /opp DG 1 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /main DA -9 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /opp DG -10 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /opp DG -10 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /opp DG -10 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /opp DC -9 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /opp DT -13 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /opp DG -10 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /opp DG -10 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /opp DT -11 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /opp DG -10 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /main DT 12 O2 /E ARG 362 HH22 2.881 2.130
/E LYS 363 N /opp DC -9 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /opp DA -8 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 546 N /main DA 1 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /opp DG 5 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /opp DG 5 N7 /G ARG 557 HH22 2.372 1.443
/G GLY 561 N /main DT -10 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 OG1 /main DT -10 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /main DA -9 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /opp DG 3 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /main DA 0 OP2 /G LYS 581 HZ1 3.143 2.140
61 hydrogen bonds found
21 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G twoColors true intraRes false
> select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /opp DC 18 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /main DT -16 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /main DC -15 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /opp DT 17 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /opp DC 18 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /main DC -13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /main DA -12 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /main DC -13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /main DC -13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /opp DG -10 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /main DG 9 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /opp DG -10 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /main DG 9 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /main DT 8 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /opp DA 8 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /opp DA 10 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /main DT -8 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /opp DT 12 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /opp DT 11 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /main DA -9 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.278 2.327
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /main DA 7 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /main DA -12 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /main DA -11 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /main DA -11 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /opp DG 1 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /main DA -9 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /opp DG -10 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /opp DG -10 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /opp DG -10 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /opp DC -9 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /opp DT -13 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /opp DG -10 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /opp DG -10 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /opp DT -11 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /opp DG -10 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /main DT 12 O2 /E ARG 362 HH22 2.881 2.130
/E LYS 363 N /opp DC -9 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /opp DA -8 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 546 N /main DA 1 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /opp DG 5 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /opp DG 5 N7 /G ARG 557 HH22 2.372 1.443
/G GLY 561 N /main DT -10 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 OG1 /main DT -10 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /main DA -9 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /opp DG 3 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /main DA 0 OP2 /G LYS 581 HZ1 3.143 2.140
61 hydrogen bonds found
21 strict hydrogen bonds found
> select nucleic
2291 atoms, 2469 bonds, 72 residues, 1 model selected
> hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G twoColors true slopColor
> #00f900 intraRes false select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /opp DC 18 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /main DT -16 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /main DC -15 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /opp DT 17 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /opp DC 18 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /main DC -13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /main DA -12 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /main DC -13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /main DC -13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /opp DG -10 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /main DG 9 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /opp DG -10 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /main DG 9 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /main DT 8 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /opp DA 8 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /opp DA 10 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /main DT -8 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /opp DT 12 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /opp DT 11 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /main DA -9 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.278 2.327
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /main DA 7 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /main DA -12 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /main DA -11 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /main DA -11 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /opp DG 1 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /main DA -9 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /opp DG -10 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /opp DG -10 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /opp DG -10 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /opp DC -9 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /opp DT -13 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /opp DG -10 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /opp DG -10 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /opp DT -11 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /opp DG -10 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /main DT 12 O2 /E ARG 362 HH22 2.881 2.130
/E LYS 363 N /opp DC -9 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /opp DA -8 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 546 N /main DA 1 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /opp DG 5 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /opp DG 5 N7 /G ARG 557 HH22 2.372 1.443
/G GLY 561 N /main DT -10 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 OG1 /main DT -10 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /main DA -9 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /opp DG 3 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /main DA 0 OP2 /G LYS 581 HZ1 3.143 2.140
61 hydrogen bonds found
21 strict hydrogen bonds found
> select clear
> select /main:7
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /main:8
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select /main:12@C2
1 atom, 1 residue, 1 model selected
> select /main:15
33 atoms, 35 bonds, 1 residue, 1 model selected
> select clear
> select /opp:17
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /opp:18
31 atoms, 32 bonds, 1 residue, 1 model selected
> select /opp:18
31 atoms, 32 bonds, 1 residue, 1 model selected
> select /opp:17
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /opp:18
31 atoms, 32 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select /opp:11
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select /opp:12
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /opp:10
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /opp:9
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /opp:8
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /opp:9
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /opp:1
33 atoms, 35 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /opp:0
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /opp:-2
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /opp:-4
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /opp:-8
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /opp:-9
30 atoms, 31 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /E:363@N
1 atom, 1 residue, 1 model selected
> select /opp:-9
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /E:362@N
1 atom, 1 residue, 1 model selected
> select /opp:-9
30 atoms, 31 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /opp:-11
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /opp:-10
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /E:357@N
1 atom, 1 residue, 1 model selected
> select /E:356
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"
Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 75323 atom styles
71260 atoms, 72152 bonds, 18 pseudobonds, 5940 residues, 4 models selected
> close #1
> select nucleic
1476 atoms, 1654 bonds, 72 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-
> generation2_ver31_relaxed40" dashes 6 restrict #2/A,B,C,D,E,F,G angleSlop
> 40.0 twoColors true slopColor #ff9300 intraRes false select true reveal true
> retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
78 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 no hydrogen 3.042 N/A
/A ARG 301 NH1 /H DT 10 O2 no hydrogen 2.780 N/A
/A ARG 301 NH1 /H DC 11 O4' no hydrogen 2.808 N/A
/A ARG 301 NH2 /I DT 46 O2 no hydrogen 3.419 N/A
/A ARG 301 NH2 /I DC 47 OP1 no hydrogen 3.241 N/A
/A PHE 303 N /H DC 13 OP1 no hydrogen 2.683 N/A
/A LYS 305 NZ /H DA 14 OP1 no hydrogen 3.005 N/A
/A ASN 435 ND2 /H DC 13 OP2 no hydrogen 2.896 N/A
/A ASN 436 ND2 /H DC 13 OP2 no hydrogen 3.172 N/A
/B LYS 148 NZ /I DG 19 OP1 no hydrogen 2.880 N/A
/B ARG 150 NH1 /H DG 35 O6 no hydrogen 3.317 N/A
/B ARG 150 NH1 /I DG 19 O6 no hydrogen 3.200 N/A
/B ARG 150 NH2 /H DG 35 O6 no hydrogen 2.932 N/A
/B GLY 153 N /H DT 34 OP2 no hydrogen 2.955 N/A
/B LYS 248 NZ /I DA 37 O3' no hydrogen 3.058 N/A
/B LYS 279 N /I DA 39 OP1 no hydrogen 3.012 N/A
/B ASP 280 N /I DA 39 OP1 no hydrogen 3.419 N/A
/C LYS 188 NZ /H DT 18 OP1 no hydrogen 2.597 N/A
/C ARG 219 N /I DT 41 OP1 no hydrogen 2.860 N/A
/C ARG 219 NH1 /I DT 40 OP1 no hydrogen 2.808 N/A
/C ARG 220 NH1 /H DA 15 N3 no hydrogen 3.522 N/A
/C ARG 220 NH1 /H DT 16 O2 no hydrogen 3.328 N/A
/C ARG 220 NH1 /I DT 40 O2 no hydrogen 3.062 N/A
/C TYR 223 OH /H DA 17 O3' no hydrogen 2.926 N/A
/C TYR 223 OH /H DT 18 OP1 no hydrogen 2.834 N/A
/C TYR 607 OH /H DC 32 OP2 no hydrogen 3.278 N/A
/C LYS 671 N /H DC 32 OP1 no hydrogen 2.864 N/A
/C ARG 672 N /H DC 32 OP1 no hydrogen 2.895 N/A
/C ARG 672 NH1 /I DT 25 O2 no hydrogen 2.707 N/A
/C ARG 672 NH2 /I DT 25 O2 no hydrogen 3.408 N/A
/C LYS 673 NZ /H DA 33 OP1 no hydrogen 2.886 N/A
/D LYS 168 NZ /H DA 14 N3 no hydrogen 2.838 N/A
/D SER 169 OG /H DA 14 O3' no hydrogen 3.382 N/A
/D SER 169 OG /H DA 15 OP2 no hydrogen 2.801 N/A
/D ILE 170 N /H DA 15 OP2 no hydrogen 3.077 N/A
/D SER 463 OG /I DG 30 OP1 no hydrogen 2.493 N/A
/D LYS 465 NZ /I DG 31 N7 no hydrogen 3.444 N/A
/D LYS 465 NZ /I DG 31 O6 no hydrogen 2.363 N/A
/D LYS 465 NZ /I DG 32 O6 no hydrogen 2.546 N/A
/E ARG 76 NH1 /H DA 17 OP1 no hydrogen 3.235 N/A
/E ARG 340 NE /I DG 19 O5' no hydrogen 3.009 N/A
/E ARG 340 NE /I DG 19 OP2 no hydrogen 2.873 N/A
/E ARG 340 NH2 /I DG 19 OP2 no hydrogen 3.300 N/A
/E TYR 341 OH /I DG 19 O3' no hydrogen 3.180 N/A
/E TYR 341 OH /I DC 20 OP1 no hydrogen 2.940 N/A
/E ARG 356 NH1 /I DT 18 OP2 no hydrogen 2.602 N/A
/E ARG 357 NH1 /I DT 16 O2 no hydrogen 2.784 N/A
/E ARG 357 NH2 /I DT 16 O2 no hydrogen 2.882 N/A
/E ARG 357 NH2 /I DT 16 O4' no hydrogen 3.135 N/A
/E GLU 358 N /H DG 41 OP1 no hydrogen 2.888 N/A
/E THR 359 OG1 /I DG 19 OP1 no hydrogen 2.802 N/A
/E ARG 362 N /I DG 19 O3' no hydrogen 3.350 N/A
/E ARG 362 NH1 /I DT 18 O2 no hydrogen 2.975 N/A
/E ARG 362 NH1 /I DG 19 O4' no hydrogen 3.022 N/A
/E ARG 362 NH2 /H DT 38 O2 no hydrogen 2.881 N/A
/E ARG 362 NH2 /H DA 39 O4' no hydrogen 3.366 N/A
/E LYS 363 N /I DC 20 OP2 no hydrogen 3.408 N/A
/E LYS 363 NZ /I DA 21 OP1 no hydrogen 2.944 N/A
/G GLY 543 N /H DA 26 OP1 no hydrogen 2.943 N/A
/G GLY 546 N /H DA 27 OP1 no hydrogen 2.915 N/A
/G LYS 547 NZ /I DG 31 O3' no hydrogen 2.870 N/A
/G LYS 547 NZ /I DG 32 OP1 no hydrogen 2.552 N/A
/G LYS 548 NZ /H DA 27 N3 no hydrogen 2.902 N/A
/G LYS 548 NZ /H DG 28 O4' no hydrogen 2.987 N/A
/G LYS 548 NZ /I DT 29 O2 no hydrogen 3.197 N/A
/G ASN 553 N /I DG 32 OP2 no hydrogen 2.957 N/A
/G ARG 557 NH1 /I DG 34 O6 no hydrogen 2.913 N/A
/G ARG 557 NH1 /I DT 35 O4 no hydrogen 3.519 N/A
/G ARG 557 NH2 /I DG 34 N7 no hydrogen 2.372 N/A
/G LYS 560 NZ /H DA 15 OP1 no hydrogen 3.180 N/A
/G GLY 561 N /H DT 16 OP2 no hydrogen 2.846 N/A
/G THR 563 N /H DT 16 OP1 no hydrogen 2.931 N/A
/G THR 563 OG1 /H DA 15 O3' no hydrogen 2.798 N/A
/G THR 563 OG1 /H DT 16 OP1 no hydrogen 3.027 N/A
/G ALA 565 N /H DA 17 OP2 no hydrogen 2.576 N/A
/G ARG 574 NH2 /I DG 32 OP1 no hydrogen 3.076 N/A
/G LYS 581 NZ /H DA 26 O5' no hydrogen 3.367 N/A
/G LYS 581 NZ /H DA 26 OP2 no hydrogen 3.143 N/A
78 hydrogen bonds found
25 strict hydrogen bonds found
> select up
1142 atoms, 1192 bonds, 81 residues, 1 model selected
> show sel atoms
> ui tool show H-Bonds
> ui tool show "Add Hydrogens"
> addh #!2
Summary of feedback from adding hydrogens to
ylODC_54bpOriC061_rev31_PostPhenix.pdb #2
---
warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners
Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond
partners
notes | Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain A determined from SEQRES records
Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain B determined
from SEQRES records
No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
C; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
D; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
E; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
F; guessing termini instead
No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
G; guessing termini instead
Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain H determined
from SEQRES records
Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain I determined
from SEQRES records
Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C
THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL
34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F
GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439
Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127,
/D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL
439
Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU
685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D
ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS
335, /G ASN 434, /G LYS 602
Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D
MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS
602, /G GLY 207, /G HIS 335, /G ASN 434
Chain-initial residues that are not actual 5' termini: /I DG 13
Missing OXT added to C-terminal residue /B LEU 507
Missing OXT added to C-terminal residue /C ARG 29
Missing OXT added to C-terminal residue /D SER 123
Missing OXT added to C-terminal residue /D MET 285
Missing OXT added to C-terminal residue /D LEU 420
8 messages similar to the above omitted
3054 hydrogen bonds
Adding 'H' to /C ASN 72
Adding 'H' to /D GLN 127
Adding 'H' to /D LEU 296
Adding 'H' to /D PHE 436
Adding 'H' to /E ASP 319
4 messages similar to the above omitted
24712 hydrogens added
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-
> generation2_ver31_relaxed40" restrict #2/A,B,C,D,E,F,G angleSlop 40.0
> twoColors true slopColor #ff9300 intraRes false select true reveal true log
> true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
139 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A LYS 300 NZ /A ASN 436 OD1 /A LYS 300 HZ1 3.118 2.399
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 N /A ARG 431 O /A LYS 305 H 2.798 1.912
/A LYS 305 NZ /A GLU 421 OE1 /A LYS 305 HZ2 3.041 2.143
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /A ASN 436 OD1 /A ASN 435 HD21 3.103 2.697
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/A LYS 439 N /A ASN 435 O /A LYS 439 H 3.001 2.009
/A LEU 440 N /A ASN 436 O /A LEU 440 H 2.894 1.926
/A ARG 696 NH2 /G GLY 546 O /A ARG 696 HH21 3.117 2.584
/B LYS 148 N /B PHE 144 O /B LYS 148 H 2.920 2.035
/B LYS 148 NZ /E ARG 340 O /B LYS 148 HZ1 2.840 1.919
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B ASN 252 N /B LYS 248 O /B ASN 252 H 2.859 1.943
/B ASN 252 ND2 /B LYS 248 O /B ASN 252 HD21 2.823 2.421
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B LYS 279 NZ /B ASN 275 O /B LYS 279 HZ1 3.083 2.418
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/B ASP 282 N /B ASP 280 OD1 /B ASP 282 H 3.192 2.326
/B LEU 284 N /B ASP 280 O /B LEU 284 H 2.837 1.850
/C LYS 188 N /C SER 186 OG /C LYS 188 H 3.325 2.447
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C LYS 192 N /C LYS 188 O /C LYS 192 H 2.878 1.920
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NE /C GLU 212 OE1 /C ARG 219 HE 3.259 2.637
/C ARG 219 NE /C GLU 212 OE2 /C ARG 219 HE 2.841 2.024
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 219 NH2 /C GLU 212 OE1 /C ARG 219 HH21 2.795 2.099
/C ARG 220 N /C ASP 218 OD1 /C ARG 220 H 2.980 2.018
/C ARG 220 NE /C ASP 218 OD1 /C ARG 220 HE 2.810 1.851
/C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C ARG 220 NH2 /C ASP 218 OD2 /C ARG 220 HH21 2.856 1.862
/C LYS 222 N /C ARG 219 O /C LYS 222 H 3.430 2.524
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C THR 670 OG1 /C LYS 673 O /C THR 670 HG1 2.628 1.854
/C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /B ARG 152 O /C LYS 673 HZ3 3.238 2.551
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/C SER 676 N /C LYS 673 O /C SER 676 H 3.091 2.178
/D LYS 144 NZ /G LYS 560 O /D LYS 144 HZ1 3.005 2.080
/D ARG 148 NE /G GLY 561 O /D ARG 148 HE 3.310 2.528
/D ARG 148 NH1 /D LYS 168 O /D ARG 148 HH12 2.488 1.669
/D ARG 148 NH2 /D LYS 168 O /D ARG 148 HH22 2.570 1.792
/D ARG 148 NH2 /G GLY 561 O /D ARG 148 HH21 2.721 1.730
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 N /D ASN 167 OD1 /D SER 169 H 3.368 2.513
/D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D THR 173 N /D SER 169 O /D THR 173 H 2.884 1.953
/D THR 173 OG1 /D SER 169 O /D THR 173 HG1 2.830 1.908
/D LEU 174 N /D ILE 170 O /D LEU 174 H 2.877 1.880
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/D ARG 466 N /D SER 463 O /D ARG 466 H 2.968 2.378
/D ARG 466 N /D SER 463 OG /D ARG 466 H 3.160 2.176
/D VAL 467 N /D SER 463 O /D VAL 467 H 2.848 1.922
/D ALA 468 N /D LYS 465 O /D ALA 468 H 3.107 2.545
/D LYS 469 N /D LYS 465 O /D LYS 469 H 3.084 2.242
/E ARG 76 NE /E GLN 80 OE1 /E ARG 76 HE 2.849 1.855
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 76 NH2 /C ASP 218 OD2 /E ARG 76 HH22 3.505 2.561
/E ARG 76 NH2 /E GLN 80 OE1 /E ARG 76 HH21 3.522 2.773
/E GLN 80 N /E ARG 76 O /E GLN 80 H 2.915 1.931
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 N /E PRO 338 O /E TYR 341 H 3.454 2.618
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 344 N /E TYR 341 O /E ARG 344 H 2.933 2.330
/E ARG 344 NH1 /E THR 359 O /E ARG 344 HH11 3.312 2.421
/E PHE 345 N /E TYR 341 O /E PHE 345 H 3.133 2.333
/E LYS 350 NZ /E GLU 358 OE2 /E LYS 350 HZ1 2.768 1.940
/E ARG 356 NE /B ASP 145 OD1 /E ARG 356 HE 2.892 2.039
/E ARG 356 NH1 /I DT 18 OP2 /E ARG 356 HH11 2.602 1.912
/E ARG 356 NH2 /B ASP 145 O /E ARG 356 HH21 2.568 1.841
/E ARG 356 NH2 /B ASP 145 OD1 /E ARG 356 HH21 3.006 2.208
/E ARG 356 NH2 /B THR 149 OG1 /E ARG 356 HH22 3.252 2.468
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 N /E ARG 357 O /E THR 359 H 3.010 2.141
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G THR 542 N /G LYS 581 O /G THR 542 H 2.775 1.833
/G THR 542 OG1 /G LYS 581 O /G THR 542 HG1 3.224 2.270
/G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343
/G CYS 545 SG /G GLY 543 O /G CYS 545 HG 3.840 2.525
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236
/G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ASN 553 ND2 /G GLY 572 O /G ASN 553 HD22 2.832 2.022
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601
/G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G VAL 570 N /G ASN 553 O /G VAL 570 H 3.200 2.301
/G TYR 571 N /G ASN 553 OD1 /G TYR 571 H 3.237 2.453
/G ARG 574 NH2 /G GLY 551 O /G ARG 574 HH22 2.887 1.879
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G ASP 576 N /G ARG 574 O /G ASP 576 H 2.809 1.912
/G LYS 581 N /G THR 542 O /G LYS 581 H 3.429 2.627
/G LYS 581 N /G GLY 543 O /G LYS 581 H 3.308 2.380
/G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
139 hydrogen bonds found
44 strict hydrogen bonds found
> select up
2686 atoms, 2716 bonds, 122 residues, 1 model selected
> show sel atoms
> select nucleic
2291 atoms, 2469 bonds, 72 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-
> generation2_ver31_relaxed40" restrict #2/A,B,C,D,E,F,G angleSlop 40.0
> twoColors true slopColor #ff9300 intraRes false select true reveal true log
> true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
75 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 356 NH1 /I DT 18 OP2 /E ARG 356 HH11 2.602 1.912
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236
/G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601
/G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
75 hydrogen bonds found
21 strict hydrogen bonds found
> select up
1974 atoms, 2022 bonds, 80 residues, 1 model selected
> show sel atoms
> select clear
> select nucleic
2291 atoms, 2469 bonds, 72 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_ver31" dashes
> 6 restrict #2/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false
> select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
61 hydrogen bonds found
21 strict hydrogen bonds found
> select clear
> select ~sel & ##selected
Nothing selected
> select ~nucleic
47733 atoms, 48183 bonds, 11 pseudobonds, 2978 residues, 3 models selected
> hide sel cartoons
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
> select /I:18
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /I:16
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide atoms
> select nucleic
2291 atoms, 2469 bonds, 72 residues, 1 model selected
> hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G angleSlop 40.0 twoColors true
> slopColor #ff9300 intraRes false select true reveal true retainCurrent true
> log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
75 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 356 NH1 /I DT 18 OP2 /E ARG 356 HH11 2.602 1.912
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236
/G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601
/G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
75 hydrogen bonds found
21 strict hydrogen bonds found
> select up
1974 atoms, 2022 bonds, 80 residues, 1 model selected
> show sel atoms
> select nucleic
2291 atoms, 2469 bonds, 72 residues, 1 model selected
> show sel atoms
> hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G twoColors true slopColor
> #00f900 intraRes false select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096
/A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937
/A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918
/A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726
/A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383
/A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713
/A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074
/A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911
/A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251
/B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062
/B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492
/B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518
/B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954
/B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965
/B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307
/B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176
/B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439
/C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602
/C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859
/C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044
/C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600
/C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380
/C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064
/C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327
/C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905
/C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845
/C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771
/C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972
/D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847
/D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842
/D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202
/D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565
/D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498
/D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684
/E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257
/E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192
/E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974
/E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551
/E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219
/E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882
/E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025
/E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386
/E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905
/E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243
/E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344
/E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081
/E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183
/E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130
/E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442
/E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968
/G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028
/G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558
/G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248
/G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079
/G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906
/G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443
/G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111
/G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078
/G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574
/G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128
/G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140
61 hydrogen bonds found
21 strict hydrogen bonds found
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
> select /I:17
32 atoms, 34 bonds, 1 residue, 1 model selected
> select clear
> select /H:26
32 atoms, 34 bonds, 1 residue, 1 model selected
> ui tool show "Renumber Residues"
> renumber /H start -16
37 residues renumbered
> renumber /H start -18
37 residues renumbered
> renumber /I start -16
35 residues renumbered
> select /I
1121 atoms, 1207 bonds, 35 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel opp
Chain IDs of 35 residues changed
> select /H
1170 atoms, 1262 bonds, 37 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel main
Chain IDs of 37 residues changed
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
> select /opp:-13
32 atoms, 33 bonds, 1 residue, 1 model selected
> select clear
> close #2
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb"
Chain information for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 24882 atom styles
23363 atoms, 23801 bonds, 15 pseudobonds, 2924 residues, 2 models selected
> select ~nucleic
23491 atoms, 23933 bonds, 16 pseudobonds, 2932 residues, 3 models selected
> hide sel cartoons
> select nucleic
1391 atoms, 1559 bonds, 68 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
> dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor
> #ff9300 intraRes false select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
50 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A GLN 306 NE2 /I DG 53 O3' no hydrogen 3.342 N/A
/A ASN 436 ND2 /H DA 10 OP1 no hydrogen 2.810 N/A
/B LYS 148 NZ /I DA 28 OP1 no hydrogen 3.208 N/A
/B LYS 279 N /I DA 48 OP1 no hydrogen 3.110 N/A
/C LYS 188 NZ /H DC 15 OP1 no hydrogen 3.176 N/A
/C ARG 219 NH1 /I DT 49 OP2 no hydrogen 3.015 N/A
/C ARG 220 NH1 /H DT 13 O2 no hydrogen 3.388 N/A
/C ARG 220 NH1 /I DT 49 O2 no hydrogen 3.296 N/A
/C TYR 223 OH /H DC 15 OP1 no hydrogen 2.762 N/A
/C TYR 607 OH /H DC 29 OP2 no hydrogen 3.098 N/A
/C ARG 672 N /H DC 29 OP1 no hydrogen 3.388 N/A
/C ARG 672 NH1 /I DT 34 O2 no hydrogen 2.806 N/A
/C ARG 672 NH2 /I DT 34 O2 no hydrogen 2.902 N/A
/C ARG 672 NH2 /I DT 34 O4' no hydrogen 3.185 N/A
/C LYS 673 NZ /H DT 30 OP1 no hydrogen 3.030 N/A
/D LYS 168 NZ /H DT 11 O2 no hydrogen 2.564 N/A
/D SER 169 OG /H DA 12 OP1 no hydrogen 3.284 N/A
/D SER 463 OG /I DT 39 OP2 no hydrogen 2.803 N/A
/D LYS 465 NZ /I DG 40 N7 no hydrogen 3.514 N/A
/D LYS 465 NZ /I DG 40 O6 no hydrogen 3.045 N/A
/D LYS 465 NZ /I DG 41 O6 no hydrogen 3.189 N/A
/E ARG 76 NH1 /H DG 14 OP1 no hydrogen 2.908 N/A
/E ARG 340 NH1 /I DA 28 OP2 no hydrogen 3.135 N/A
/E ARG 356 NH1 /I DT 27 OP2 no hydrogen 2.946 N/A
/E ARG 357 N /I DT 27 OP1 no hydrogen 3.073 N/A
/E ARG 357 NH1 /I DT 25 O2 no hydrogen 2.761 N/A
/E ARG 357 NH2 /I DT 25 O2 no hydrogen 2.690 N/A
/E GLU 358 N /H DG 38 OP1 no hydrogen 3.275 N/A
/E THR 359 OG1 /I DA 28 OP1 no hydrogen 2.552 N/A
/E ARG 362 N /I DG 29 OP2 no hydrogen 2.892 N/A
/E ARG 362 NH1 /H DC 35 O4' no hydrogen 3.369 N/A
/E ARG 362 NH2 /H DC 35 O2 no hydrogen 3.076 N/A
/E ARG 362 NH2 /H DA 36 O4' no hydrogen 3.065 N/A
/E LYS 363 N /I DG 29 OP2 no hydrogen 3.221 N/A
/E LYS 363 NZ /I DG 30 OP1 no hydrogen 2.954 N/A
/E LYS 363 NZ /I DG 30 OP2 no hydrogen 2.890 N/A
/G THR 542 OG1 /H DA 23 OP1 no hydrogen 3.290 N/A
/G LYS 547 NZ /I DG 41 OP1 no hydrogen 3.303 N/A
/G LYS 548 NZ /H DT 24 O2 no hydrogen 2.747 N/A
/G LYS 548 NZ /H DC 25 O4' no hydrogen 2.889 N/A
/G LYS 548 NZ /I DT 38 O2 no hydrogen 3.045 N/A
/G ASN 553 N /I DG 41 OP2 no hydrogen 3.220 N/A
/G ARG 557 NH1 /I DG 44 N7 no hydrogen 3.403 N/A
/G ARG 557 NH1 /I DG 44 O6 no hydrogen 2.566 N/A
/G ARG 557 NH2 /I DG 44 N7 no hydrogen 3.082 N/A
/G LYS 560 NZ /H DA 12 OP2 no hydrogen 2.981 N/A
/G GLY 561 N /H DT 13 OP1 no hydrogen 2.977 N/A
/G THR 563 N /H DT 13 OP2 no hydrogen 3.051 N/A
/G GLY 564 N /H DT 13 OP2 no hydrogen 2.948 N/A
/G ALA 565 N /H DG 14 OP2 no hydrogen 3.032 N/A
50 hydrogen bonds found
13 strict hydrogen bonds found
> ui tool show "Add Hydrogens"
> addh #!1
Summary of feedback from adding hydrogens to
ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1
---
warning | Not adding hydrogens to /I DA 22 P because it is missing heavy-atom bond partners
notes | No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1) chain A; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1)
chain B; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1)
chain C; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1)
chain D; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1)
chain E; guessing termini instead
4 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C
THR 6, /D PRO 33, /E MET 1, /F PRO 179, /G PRO 93
Chain-initial residues that are not actual N termini: /B VAL 396, /B VAL 444,
/B LYS 489, /C ASN 72, /D ASN 128, /D GLY 162, /D LEU 296, /D PHE 436, /E GLU
217, /E ASP 319, /F SER 313, /G ALA 213, /G THR 386, /G VAL 439, /G ASN 461
Chain-final residues that are actual C termini: /A LEU 718, /C LEU 685
Chain-final residues that are not actual C termini: /B GLU 504, /B GLU 386, /B
HIS 420, /B VAL 479, /C ARG 29, /D ARG 510, /D SER 123, /D LEU 159, /D MET
285, /D LEU 420, /E ASN 464, /E ALA 210, /E LEU 304, /F GLN 351, /F THR 307,
/G LEU 604, /G GLY 207, /G HIS 335, /G GLN 433, /G PHE 457
2714 hydrogen bonds
Adding 'H' to /B VAL 396
Adding 'H' to /B VAL 444
Adding 'H' to /B LYS 489
Adding 'H' to /C ASN 72
Adding 'H' to /D ASN 128
10 messages similar to the above omitted
/B GLU 504 is not terminus, removing H atom from 'C'
/D ARG 510 is not terminus, removing H atom from 'C'
/E ASN 464 is not terminus, removing H atom from 'C'
/F GLN 351 is not terminus, removing H atom from 'C'
/G LEU 604 is not terminus, removing H atom from 'C'
24328 hydrogens added
> select clear
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true
> slopColor #ff9300 intraRes false select true reveal true retainCurrent true
> log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
49 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A GLN 306 NE2 /I DG 53 O3' /A GLN 306 HE22 3.342 2.769
/A ASN 436 ND2 /H DA 10 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /I DA 28 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /I DA 48 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /H DC 15 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 NH1 /I DT 49 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /H DT 13 O2 /C ARG 220 HH11 3.388 2.481
/C ARG 220 NH1 /I DT 49 O2 /C ARG 220 HH11 3.296 2.935
/C TYR 223 OH /H DC 15 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /H DC 29 OP2 /C TYR 607 HH 3.098 2.200
/C ARG 672 N /H DC 29 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /I DT 34 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /I DT 34 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /I DT 34 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /H DT 30 OP1 /C LYS 673 HZ1 3.030 2.116
/D LYS 168 NZ /H DT 11 O2 /D LYS 168 HZ1 2.564 2.050
/D SER 169 OG /H DA 12 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /I DT 39 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /I DG 40 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /I DG 40 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /I DG 41 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /H DG 14 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /I DA 28 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /I DT 27 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /I DT 27 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /I DT 25 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /I DT 25 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /H DG 38 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /I DA 28 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /I DG 29 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH1 /H DC 35 O4' /E ARG 362 HH12 3.369 2.780
/E ARG 362 NH2 /H DC 35 O2 /E ARG 362 HH22 3.076 2.066
/E ARG 362 NH2 /H DA 36 O4' /E ARG 362 HH21 3.065 2.496
/E LYS 363 N /I DG 29 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /I DG 30 OP1 /E LYS 363 HZ3 2.954 2.284
/E LYS 363 NZ /I DG 30 OP2 /E LYS 363 HZ1 2.890 1.985
/G GLY 546 N /H DT 24 OP1 /G GLY 546 H 3.276 2.580
/G LYS 547 NZ /I DG 41 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /H DT 24 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /H DC 25 O4' /G LYS 548 HZ2 2.889 2.196
/G LYS 548 NZ /I DT 38 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /I DG 41 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /I DG 44 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH1 /I DG 44 O6 /G ARG 557 HH12 2.566 1.988
/G ARG 557 NH2 /I DG 44 N7 /G ARG 557 HH22 3.082 2.292
/G LYS 560 NZ /H DA 12 OP2 /G LYS 560 HZ1 2.981 2.268
/G GLY 561 N /H DT 13 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /H DT 13 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /H DG 14 OP2 /G ALA 565 H 3.032 2.059
49 hydrogen bonds found
8 strict hydrogen bonds found
> select clear
> hide atoms
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> show sel atoms
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
> restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor #ff9300
> intraRes false select true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
49 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A GLN 306 NE2 /I DG 53 O3' /A GLN 306 HE22 3.342 2.769
/A ASN 436 ND2 /H DA 10 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /I DA 28 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /I DA 48 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /H DC 15 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 NH1 /I DT 49 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /H DT 13 O2 /C ARG 220 HH11 3.388 2.481
/C ARG 220 NH1 /I DT 49 O2 /C ARG 220 HH11 3.296 2.935
/C TYR 223 OH /H DC 15 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /H DC 29 OP2 /C TYR 607 HH 3.098 2.200
/C ARG 672 N /H DC 29 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /I DT 34 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /I DT 34 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /I DT 34 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /H DT 30 OP1 /C LYS 673 HZ1 3.030 2.116
/D LYS 168 NZ /H DT 11 O2 /D LYS 168 HZ1 2.564 2.050
/D SER 169 OG /H DA 12 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /I DT 39 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /I DG 40 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /I DG 40 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /I DG 41 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /H DG 14 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /I DA 28 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /I DT 27 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /I DT 27 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /I DT 25 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /I DT 25 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /H DG 38 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /I DA 28 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /I DG 29 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH1 /H DC 35 O4' /E ARG 362 HH12 3.369 2.780
/E ARG 362 NH2 /H DC 35 O2 /E ARG 362 HH22 3.076 2.066
/E ARG 362 NH2 /H DA 36 O4' /E ARG 362 HH21 3.065 2.496
/E LYS 363 N /I DG 29 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /I DG 30 OP1 /E LYS 363 HZ3 2.954 2.284
/E LYS 363 NZ /I DG 30 OP2 /E LYS 363 HZ1 2.890 1.985
/G GLY 546 N /H DT 24 OP1 /G GLY 546 H 3.276 2.580
/G LYS 547 NZ /I DG 41 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /H DT 24 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /H DC 25 O4' /G LYS 548 HZ2 2.889 2.196
/G LYS 548 NZ /I DT 38 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /I DG 41 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /I DG 44 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH1 /I DG 44 O6 /G ARG 557 HH12 2.566 1.988
/G ARG 557 NH2 /I DG 44 N7 /G ARG 557 HH22 3.082 2.292
/G LYS 560 NZ /H DA 12 OP2 /G LYS 560 HZ1 2.981 2.268
/G GLY 561 N /H DT 13 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /H DT 13 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /H DG 14 OP2 /G ALA 565 H 3.032 2.059
49 hydrogen bonds found
8 strict hydrogen bonds found
> select up
1476 atoms, 1511 bonds, 59 residues, 1 model selected
> show sel atoms
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20" dashes 6
> restrict #1/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false
> select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
39 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ASN 436 ND2 /H DA 10 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /I DA 28 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /I DA 48 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /H DC 15 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 NH1 /I DT 49 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /H DT 13 O2 /C ARG 220 HH11 3.388 2.481
/C TYR 223 OH /H DC 15 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /H DC 29 OP2 /C TYR 607 HH 3.098 2.200
/C ARG 672 N /H DC 29 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /I DT 34 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /I DT 34 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /I DT 34 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /H DT 30 OP1 /C LYS 673 HZ1 3.030 2.116
/D SER 169 OG /H DA 12 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /I DT 39 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /I DG 40 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /I DG 40 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /I DG 41 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /H DG 14 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /I DA 28 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /I DT 27 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /I DT 27 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /I DT 25 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /I DT 25 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /H DG 38 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /I DA 28 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /I DG 29 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH2 /H DC 35 O2 /E ARG 362 HH22 3.076 2.066
/E LYS 363 N /I DG 29 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /I DG 30 OP2 /E LYS 363 HZ1 2.890 1.985
/G LYS 547 NZ /I DG 41 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /H DT 24 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /I DT 38 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /I DG 41 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /I DG 44 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH2 /I DG 44 N7 /G ARG 557 HH22 3.082 2.292
/G GLY 561 N /H DT 13 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /H DT 13 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /H DG 14 OP2 /G ALA 565 H 3.032 2.059
39 hydrogen bonds found
8 strict hydrogen bonds found
> select clear
> select /I:38
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /H:23
32 atoms, 34 bonds, 1 residue, 1 model selected
> ui tool show "Renumber Residues"
> renumber /H start -18
34 residues renumbered
> renumber /H start -17
34 residues renumbered
> select /I:39
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /I:38
32 atoms, 33 bonds, 1 residue, 1 model selected
> renumber /I start -16
34 residues renumbered
> select /H
1060 atoms, 1139 bonds, 34 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel main
Chain IDs of 34 residues changed
> select /I
1098 atoms, 1187 bonds, 34 residues, 1 model selected
> changechains sel opp
Chain IDs of 34 residues changed
> select clear
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
> dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor
> #ff9300 intraRes false select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 40 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
49 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A GLN 306 NE2 /opp DG 15 O3' /A GLN 306 HE22 3.342 2.769
/A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481
/C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.296 2.935
/C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116
/D LYS 168 NZ /main DT -12 O2 /D LYS 168 HZ1 2.564 2.050
/D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH1 /main DC 12 O4' /E ARG 362 HH12 3.369 2.780
/E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066
/E ARG 362 NH2 /main DA 13 O4' /E ARG 362 HH21 3.065 2.496
/E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /opp DG -8 OP1 /E LYS 363 HZ3 2.954 2.284
/E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985
/G GLY 546 N /main DT 1 OP1 /G GLY 546 H 3.276 2.580
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /main DC 2 O4' /G LYS 548 HZ2 2.889 2.196
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH1 /opp DG 6 O6 /G ARG 557 HH12 2.566 1.988
/G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292
/G LYS 560 NZ /main DA -11 OP2 /G LYS 560 HZ1 2.981 2.268
/G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059
49 hydrogen bonds found
8 strict hydrogen bonds found
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20" dashes 6
> restrict #1/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false
> select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
39 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481
/C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116
/D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066
/E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292
/G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059
39 hydrogen bonds found
8 strict hydrogen bonds found
> select clear
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20.cxs"
> select /A:303
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select /main:-13
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
> dashes 6 restrict #1/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0 twoColors
> true slopColor #ff9300 intraRes false select true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 40 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
53 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A GLN 306 NE2 /opp DG 15 O3' /A GLN 306 HE22 3.342 2.769
/A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 N /opp DA 12 OP1 /C ARG 219 H 3.467 2.499
/C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481
/C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.296 2.935
/C TYR 223 OH /main DG -9 O3' /C TYR 223 HH 3.522 2.887
/C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200
/C LYS 671 N /main DC 6 OP1 /C LYS 671 H 3.429 2.701
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116
/D LYS 168 NZ /main DT -12 O2 /D LYS 168 HZ1 2.564 2.050
/D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /opp DA -10 O3' /E ARG 362 H 3.515 2.618
/E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH1 /main DC 12 O4' /E ARG 362 HH12 3.369 2.780
/E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066
/E ARG 362 NH2 /main DA 13 O4' /E ARG 362 HH21 3.065 2.496
/E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /opp DG -8 OP1 /E LYS 363 HZ3 2.954 2.284
/E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985
/G GLY 546 N /main DT 1 OP1 /G GLY 546 H 3.276 2.580
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /main DC 2 O4' /G LYS 548 HZ2 2.889 2.196
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH1 /opp DG 6 O6 /G ARG 557 HH12 2.566 1.988
/G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292
/G LYS 560 NZ /main DA -11 OP2 /G LYS 560 HZ1 2.981 2.268
/G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059
53 hydrogen bonds found
8 strict hydrogen bonds found
> select up
1530 atoms, 1568 bonds, 61 residues, 1 model selected
> show sel atoms
> select clear
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20" dashes 6
> restrict #1/A,B,C,D,E,F,G distSlop 0.5 twoColors true slopColor #00f900
> intraRes false select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
42 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 N /opp DA 12 OP1 /C ARG 219 H 3.467 2.499
/C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481
/C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200
/C LYS 671 N /main DC 6 OP1 /C LYS 671 H 3.429 2.701
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116
/D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /opp DA -10 O3' /E ARG 362 H 3.515 2.618
/E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066
/E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292
/G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059
42 hydrogen bonds found
8 strict hydrogen bonds found
> select up
1335 atoms, 1364 bonds, 53 residues, 1 model selected
> show sel atoms
> select clear
> select /A:436-436
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:435-436
28 atoms, 27 bonds, 2 residues, 1 model selected
> show sel atoms
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> select clear
> show cartoons
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
> dashes 6 restrict #1/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0 twoColors
> true slopColor #ff9300 intraRes false select true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 40 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
53 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A GLN 306 NE2 /opp DG 15 O3' /A GLN 306 HE22 3.342 2.769
/A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 N /opp DA 12 OP1 /C ARG 219 H 3.467 2.499
/C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481
/C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.296 2.935
/C TYR 223 OH /main DG -9 O3' /C TYR 223 HH 3.522 2.887
/C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200
/C LYS 671 N /main DC 6 OP1 /C LYS 671 H 3.429 2.701
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116
/D LYS 168 NZ /main DT -12 O2 /D LYS 168 HZ1 2.564 2.050
/D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /opp DA -10 O3' /E ARG 362 H 3.515 2.618
/E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH1 /main DC 12 O4' /E ARG 362 HH12 3.369 2.780
/E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066
/E ARG 362 NH2 /main DA 13 O4' /E ARG 362 HH21 3.065 2.496
/E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /opp DG -8 OP1 /E LYS 363 HZ3 2.954 2.284
/E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985
/G GLY 546 N /main DT 1 OP1 /G GLY 546 H 3.276 2.580
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /main DC 2 O4' /G LYS 548 HZ2 2.889 2.196
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH1 /opp DG 6 O6 /G ARG 557 HH12 2.566 1.988
/G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292
/G LYS 560 NZ /main DA -11 OP2 /G LYS 560 HZ1 2.981 2.268
/G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059
53 hydrogen bonds found
8 strict hydrogen bonds found
> select clear
> select ~nucleic
47052 atoms, 47494 bonds, 16 pseudobonds, 2932 residues, 3 models selected
> hide sel cartoons
> select clear
> select /main:-13
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select /A:301,306,303,435,436,305
111 atoms, 108 bonds, 6 residues, 1 model selected
> show sel atoms
> select /B:279,280,248,153,150,148
109 atoms, 104 bonds, 6 residues, 1 model selected
> show sel atoms
> select /C:219,220,223,188,671-673
159 atoms, 156 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> select /D:168,169,465,463
66 atoms, 63 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select /E:76,341,363,359,362,340,356,357,358
192 atoms, 189 bonds, 9 residues, 1 model selected
> show sel atoms
> select clear
> select /G:560,561,563,565,557,547,548,543,581,546
157 atoms, 150 bonds, 10 residues, 1 model selected
> show sel atoms
> select clear
> select /main:-1
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /main:0
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /main:-1
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
Drag select of 2 atoms, 2 bonds
> select clear
> select /A:305@NZ
1 atom, 1 residue, 1 model selected
> select /main:-12
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /main:-13@C3'
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select /main:-11
32 atoms, 34 bonds, 1 residue, 1 model selected
> select nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20" dashes 6
> restrict #1/A,B,C,D,E,F,G distSlop 0.5 twoColors true slopColor #00f900
> intraRes false select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
42 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833
/B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369
/B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192
/C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193
/C ARG 219 N /opp DA 12 OP1 /C ARG 219 H 3.467 2.499
/C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053
/C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481
/C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806
/C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200
/C LYS 671 N /main DC 6 OP1 /C LYS 671 H 3.429 2.701
/C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439
/C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902
/C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042
/C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472
/C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116
/D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325
/D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844
/D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654
/D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260
/D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368
/E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005
/E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272
/E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163
/E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081
/E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945
/E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846
/E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276
/E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830
/E ARG 362 N /opp DA -10 O3' /E ARG 362 H 3.515 2.618
/E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000
/E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066
/E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221
/E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985
/G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294
/G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031
/G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142
/G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217
/G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708
/G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292
/G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057
/G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249
/G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059
42 hydrogen bonds found
8 strict hydrogen bonds found
> select clear
> select /main:-9
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /main:-8
30 atoms, 31 bonds, 1 residue, 1 model selected
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"
Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> select #2
24882 atoms, 25492 bonds, 16 pseudobonds, 3000 residues, 3 models selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 24882 atom styles
> newcolor #2/A #2/B #2/C #2/D #2/E #2/F #2/G #2/H #2/I
> color sel byhetero
> hide sel atoms
> select clear
> select #2 & nucleic
1391 atoms, 1559 bonds, 68 residues, 1 model selected
> hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 twoColors true
> slopColor #00f900 intraRes false select true reveal true retainCurrent true
> log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
46 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1 no hydrogen 2.810 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 no hydrogen 3.208 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1 no hydrogen 3.110 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 no hydrogen 3.176 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1 no hydrogen 3.467 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2 no hydrogen 3.015 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2 no hydrogen 3.388 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 no hydrogen 2.762 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2 no hydrogen 3.098 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 no hydrogen 3.388 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 no hydrogen 2.806 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 no hydrogen 2.902 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4' no hydrogen 3.185 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1 no hydrogen 3.030 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2 no hydrogen 2.564 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1 no hydrogen 3.284 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2 no hydrogen 2.803 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7 no hydrogen 3.514 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6 no hydrogen 3.045 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6 no hydrogen 3.189 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1 no hydrogen 2.908 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2 no hydrogen 3.135 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2 no hydrogen 2.946 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1 no hydrogen 3.073 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 no hydrogen 2.761 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 no hydrogen 2.690 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1 no hydrogen 3.275 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 no hydrogen 2.552 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3' no hydrogen 3.515 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 no hydrogen 2.892 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2 no hydrogen 3.076 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 no hydrogen 3.221 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2 no hydrogen 2.890 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 542 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 23 OP1 no hydrogen 3.290 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1 no hydrogen 3.276 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1 no hydrogen 3.303 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2 no hydrogen 2.747 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4' no hydrogen 2.889 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2 no hydrogen 3.045 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2 no hydrogen 3.220 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 no hydrogen 3.403 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 no hydrogen 3.082 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2 no hydrogen 2.981 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1 no hydrogen 2.977 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 no hydrogen 3.051 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2 no hydrogen 3.032 N/A
46 hydrogen bonds found
13 strict hydrogen bonds found
> select up
840 atoms, 876 bonds, 59 residues, 1 model selected
> show sel atoms
> select #2 & ~nucleic
23491 atoms, 23933 bonds, 16 pseudobonds, 2932 residues, 3 models selected
> hide sel cartoons
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #2 & nucleic
1391 atoms, 1559 bonds, 68 residues, 1 model selected
> hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0
> twoColors true slopColor #ff9300 intraRes false select true reveal true
> retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 40 degrees
Models used:
2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
55 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 54 N3 no hydrogen 3.290 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 NE2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 53 O3' no hydrogen 3.342 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1 no hydrogen 2.810 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 no hydrogen 3.208 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1 no hydrogen 3.110 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 no hydrogen 3.176 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1 no hydrogen 3.467 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2 no hydrogen 3.015 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2 no hydrogen 3.388 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 O2 no hydrogen 3.296 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 O3' no hydrogen 3.522 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 no hydrogen 2.762 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2 no hydrogen 3.098 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 no hydrogen 3.388 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 no hydrogen 2.806 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 no hydrogen 2.902 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4' no hydrogen 3.185 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1 no hydrogen 3.030 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2 no hydrogen 2.564 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1 no hydrogen 3.284 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2 no hydrogen 2.803 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7 no hydrogen 3.514 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6 no hydrogen 3.045 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6 no hydrogen 3.189 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1 no hydrogen 2.908 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2 no hydrogen 3.135 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2 no hydrogen 2.946 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1 no hydrogen 3.073 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 no hydrogen 2.761 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 no hydrogen 2.690 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1 no hydrogen 3.275 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 no hydrogen 2.552 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3' no hydrogen 3.515 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 no hydrogen 2.892 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O4' no hydrogen 3.369 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2 no hydrogen 3.076 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 36 O4' no hydrogen 3.065 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 no hydrogen 3.221 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP1 no hydrogen 2.954 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2 no hydrogen 2.890 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 542 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 23 OP1 no hydrogen 3.290 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1 no hydrogen 3.276 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1 no hydrogen 3.303 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2 no hydrogen 2.747 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4' no hydrogen 2.889 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2 no hydrogen 3.045 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2 no hydrogen 3.220 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 no hydrogen 3.403 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 O6 no hydrogen 2.566 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 no hydrogen 3.082 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2 no hydrogen 2.981 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1 no hydrogen 2.977 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 no hydrogen 3.051 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 564 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 no hydrogen 2.948 N/A
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2 no hydrogen 3.032 N/A
55 hydrogen bonds found
13 strict hydrogen bonds found
> select up
929 atoms, 972 bonds, 65 residues, 1 model selected
> show sel atoms
> select clear
> ui tool show "Add Hydrogens"
> addh #!2
Summary of feedback from adding hydrogens to
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2
---
warning | Not adding hydrogens to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 22 P because it is missing heavy-atom bond partners
notes | No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2) chain A; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2)
chain B; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2)
chain C; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2)
chain D; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2)
chain E; guessing termini instead
4 messages similar to the above omitted
Chain-initial residues that are actual N termini:
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A PRO 299,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B PRO 106,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C THR 6,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D PRO 33,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E MET 1,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F PRO 179,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G PRO 93
Chain-initial residues that are not actual N termini:
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 396,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 444,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 489,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ASN 72,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ASN 128,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D GLY 162,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 296,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D PHE 436,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 217,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASP 319,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F SER 313,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 213,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 386,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G VAL 439,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 461
Chain-final residues that are actual C termini:
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A LEU 718,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LEU 685
Chain-final residues that are not actual C termini:
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 504,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 386,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B HIS 420,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 479,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 29,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ARG 510,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 123,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 159,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D MET 285,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 420,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASN 464,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ALA 210,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LEU 304,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F GLN 351,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F THR 307,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LEU 604,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 207,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G HIS 335,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLN 433,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G PHE 457
2714 hydrogen bonds
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 396
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 444
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 489
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ASN 72
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ASN 128
10 messages similar to the above omitted
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 504 is not terminus,
removing H atom from 'C'
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ARG 510 is not terminus,
removing H atom from 'C'
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASN 464 is not terminus,
removing H atom from 'C'
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F GLN 351 is not terminus,
removing H atom from 'C'
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LEU 604 is not terminus,
removing H atom from 'C'
24328 hydrogens added
> select #2 & nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0
> twoColors true slopColor #ff9300 intraRes false select true reveal true
> retainCurrent true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 40 degrees
Models used:
2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
54 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 54 N3 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 HH22 3.290 2.710
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 NE2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 53 O3' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 HE22 3.342 2.769
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 HD22 2.810 1.833
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 HZ3 3.208 2.369
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 H 3.110 2.192
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 HZ1 3.176 2.193
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 H 3.467 2.499
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 HH11 3.015 2.053
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11 3.388 2.481
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11 3.296 2.935
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 O3' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH 3.522 2.887
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH 2.762 1.806
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 HH 3.098 2.200
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 H 3.429 2.701
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 H 3.388 2.439
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH12 2.806 1.902
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22 2.902 2.042
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22 3.185 2.472
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 HZ1 3.030 2.116
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 HZ1 2.564 2.050
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 HG 3.284 2.325
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 HG 2.803 1.844
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1 3.514 2.654
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1 3.045 2.260
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ2 3.189 2.368
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 HH11 2.908 2.005
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 HH11 3.135 2.272
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 HH11 2.946 2.163
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 H 3.073 2.081
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH12 2.761 1.945
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH22 2.690 1.846
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 H 3.275 2.276
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 HG1 2.552 1.830
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H 3.515 2.618
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H 2.892 2.000
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH12 3.369 2.780
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH22 3.076 2.066
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 36 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH21 3.065 2.496
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 H 3.221 2.221
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ3 2.954 2.284
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ1 2.890 1.985
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 H 3.276 2.580
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 HZ1 3.303 2.294
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ1 2.747 2.031
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ2 2.889 2.196
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ3 3.045 2.142
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 H 3.220 2.217
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12 3.403 2.708
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12 2.566 1.988
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH22 3.082 2.292
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 HZ1 2.981 2.268
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 H 2.977 2.057
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 H 3.051 2.249
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 H 3.032 2.059
54 hydrogen bonds found
8 strict hydrogen bonds found
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2 & nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> show sel atoms
> select clear
> select #2 & nucleic
2158 atoms, 2326 bonds, 68 residues, 1 model selected
> hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 twoColors true
> slopColor #00f900 intraRes false select true reveal true retainCurrent true
> log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
42 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 HD22 2.810 1.833
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 HZ3 3.208 2.369
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 H 3.110 2.192
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 HZ1 3.176 2.193
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 H 3.467 2.499
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 HH11 3.015 2.053
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11 3.388 2.481
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH 2.762 1.806
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 HH 3.098 2.200
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 H 3.429 2.701
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 H 3.388 2.439
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH12 2.806 1.902
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22 2.902 2.042
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22 3.185 2.472
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 HZ1 3.030 2.116
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 HG 3.284 2.325
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 HG 2.803 1.844
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1 3.514 2.654
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1 3.045 2.260
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ2 3.189 2.368
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 HH11 2.908 2.005
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 HH11 3.135 2.272
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 HH11 2.946 2.163
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 H 3.073 2.081
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH12 2.761 1.945
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH22 2.690 1.846
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 H 3.275 2.276
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 HG1 2.552 1.830
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H 3.515 2.618
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H 2.892 2.000
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH22 3.076 2.066
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 H 3.221 2.221
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ1 2.890 1.985
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 HZ1 3.303 2.294
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ1 2.747 2.031
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ3 3.045 2.142
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 H 3.220 2.217
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12 3.403 2.708
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH22 3.082 2.292
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 H 2.977 2.057
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 H 3.051 2.249
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 H 3.032 2.059
42 hydrogen bonds found
8 strict hydrogen bonds found
> select clear
> select #2/A:301@HH12
1 atom, 1 residue, 1 model selected
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> select #1/opp:16
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/D:168@NZ
1 atom, 1 residue, 1 model selected
> undo
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> select #1/main:-10
32 atoms, 33 bonds, 1 residue, 1 model selected
> select #1/main:-11
32 atoms, 34 bonds, 1 residue, 1 model selected
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> select #1/main:-9
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/main:-8
30 atoms, 31 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
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> hide #!2 models
> select #1/B:280@CA
1 atom, 1 residue, 1 model selected
> select #1/opp:9
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/opp:10
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show #!2 models
> hide #!1 models
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> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"
Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> hide #3
> show #3/B:248
> style sel stick
Changed 32 atom styles
> style sel stick
Changed 32 atom styles
> style sel stick
Changed 32 atom styles
> select clear
> select add #3
24882 atoms, 25492 bonds, 16 pseudobonds, 3000 residues, 3 models selected
> style sel stick
Changed 24882 atom styles
> color sel byhetero
> select #1/opp:9
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #3/B:248@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hbonds sel dashes 6 restrict #3/H,I distSlop 0.5 angleSlop 40.0 twoColors
> true slopColor #00f900 intraRes false select true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 40 degrees
Models used:
3 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> select #3/B:248@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hbonds sel dashes 6 restrict #3/H,I distSlop 0.5 angleSlop 40.0 twoColors
> true slopColor #00f900 intraRes false select true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 40 degrees
Models used:
3 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> select #1/opp:9
30 atoms, 31 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/B:248@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Add Hydrogens"
> addh #!3
Summary of feedback from adding hydrogens to
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3
---
warning | Not adding hydrogens to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/I DA 22 P because it is missing heavy-atom bond partners
notes | No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3) chain A; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3)
chain B; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3)
chain C; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3)
chain D; guessing termini instead
No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3)
chain E; guessing termini instead
4 messages similar to the above omitted
Chain-initial residues that are actual N termini:
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/A PRO 299,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B PRO 106,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C THR 6,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D PRO 33,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E MET 1,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F PRO 179,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G PRO 93
Chain-initial residues that are not actual N termini:
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 396,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 444,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B LYS 489,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ASN 72,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ASN 128,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D GLY 162,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 296,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D PHE 436,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E GLU 217,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASP 319,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F SER 313,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G ALA 213,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G THR 386,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G VAL 439,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G ASN 461
Chain-final residues that are actual C termini:
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/A LEU 718,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C LEU 685
Chain-final residues that are not actual C termini:
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 504,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 386,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B HIS 420,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 479,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ARG 29,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ARG 510,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D SER 123,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 159,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D MET 285,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 420,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASN 464,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ALA 210,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E LEU 304,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F GLN 351,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F THR 307,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LEU 604,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G GLY 207,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G HIS 335,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G GLN 433,
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G PHE 457
2713 hydrogen bonds
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 396
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 444
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B LYS 489
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ASN 72
Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ASN 128
10 messages similar to the above omitted
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 504 is not terminus,
removing H atom from 'C'
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ARG 510 is not terminus,
removing H atom from 'C'
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASN 464 is not terminus,
removing H atom from 'C'
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F GLN 351 is not terminus,
removing H atom from 'C'
ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LEU 604 is not terminus,
removing H atom from 'C'
24328 hydrogens added
> select #3/B:248@HZ2
1 atom, 1 residue, 1 model selected
> close #3
> select #1/B:279@N
1 atom, 1 residue, 1 model selected
> select #1/opp:10@P
1 atom, 1 residue, 1 model selected
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs"
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
opened ChimeraX session
> select /opp:3
33 atoms, 35 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
> session
opened ChimeraX session
> select /G:574
48 atoms, 46 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select #1/opp:3
33 atoms, 35 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/G:543@N
1 atom, 1 residue, 1 model selected
> show #!2 models
> hide #!1 models
> select #2/H:23
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/G:542@OG1
1 atom, 1 residue, 1 model selected
> hide #!2 models
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
opened ChimeraX session
> select /G:542
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select /main:-1
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /main:0
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20.cxs" format session
opened ChimeraX session
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
> session
opened ChimeraX session
> show #!2 models
> hide #!1 models
> select /G:542
28 atoms, 26 bonds, 2 residues, 2 models selected
> show sel & #!2 atoms
> select /G:543
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel & #!2 atoms
> select clear
> select #2/H:22
32 atoms, 34 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #2/H:23
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> show #!1 models
> hide #!2 models
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs" format
> session
opened ChimeraX session
> select /main:0
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
> session
opened ChimeraX session
> select #1/G:581@NZ
1 atom, 1 residue, 1 model selected
> select add #1/main:0@OP2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/G:581@NZ #1/main:0@OP2
Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/G LYS 581 NZ
and /main DA 0 OP2: 5.033Å
> select #1/G:581@NZ
1 atom, 1 residue, 1 model selected
> select add #1/main:0@OP1
2 atoms, 2 residues, 1 model selected
> distance #1/G:581@NZ #1/main:0@OP1
Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/G LYS 581 NZ
and /main DA 0 OP1: 4.742Å
> ~distance #1/G:581@NZ #1/main:0@OP1
> ~distance #1/G:581@NZ #1/main:0@OP2
> show #!2 models
> hide #!2 models
> select add #1
49210 atoms, 49820 bonds, 69 pseudobonds, 3000 residues, 4 models selected
> select subtract #1
Nothing selected
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"
Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> hide #3
> select /G:548
53 atoms, 50 bonds, 3 residues, 3 models selected
> select /G:581
53 atoms, 50 bonds, 3 residues, 3 models selected
> show sel & #!1,3 atoms
> style sel & #!1,3 stick
Changed 31 atom styles
> select #3/G:581@NZ
1 atom, 1 residue, 1 model selected
> select add #1/main:0@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/G:581@NZ #1/main:0@OP1
Distance between ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LYS 581 NZ
and ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/main DA 0 OP1: 4.358Å
> select #3/G:581@NZ
1 atom, 1 residue, 1 model selected
> select add #1/main:0@OP2
2 atoms, 2 residues, 2 models selected
> distance #3/G:581@NZ #1/main:0@OP2
Distance between ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LYS 581 NZ
and ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/main DA 0 OP2: 4.621Å
> ~distance #3/G:581@NZ #1/main:0@OP2
> ~distance #3/G:581@NZ #1/main:0@OP1
> close #3
> select #1/main:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/main:7
32 atoms, 33 bonds, 1 residue, 1 model selected
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs" format
> session
opened ChimeraX session
> select /main:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
> session
opened ChimeraX session
> select #1/main:7
32 atoms, 33 bonds, 1 residue, 1 model selected
> select #1/B:153@CA
1 atom, 1 residue, 1 model selected
> select #1/main:8
30 atoms, 31 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select #1/B:153@N
1 atom, 1 residue, 1 model selected
> select add #1/main:8@OP1
2 atoms, 2 residues, 1 model selected
> select #1/main:7
32 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/B:153@H
1 atom, 1 residue, 1 model selected
> select add #1/main:8@OP1
2 atoms, 2 residues, 1 model selected
> select #1/B:153@N
1 atom, 1 residue, 1 model selected
> select add #1/main:8@OP1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/B:153@N #1/main:8@OP1
Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/B GLY 153 N
and /main DC 8 OP1: 3.580Å
> ~distance #1/B:153@N #1/main:8@OP1
> select clear
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1/B:148@NZ
1 atom, 1 residue, 1 model selected
> select #1/opp:-10
32 atoms, 34 bonds, 1 residue, 1 model selected
> select #1/opp:-9
33 atoms, 35 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/opp:-10
32 atoms, 34 bonds, 1 residue, 1 model selected
> select #1/opp:-11
32 atoms, 33 bonds, 1 residue, 1 model selected
> select #1/opp:-10
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/E:358@N
1 atom, 1 residue, 1 model selected
> select #1/main:-13
32 atoms, 34 bonds, 1 residue, 1 model selected
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs" format
> session
opened ChimeraX session
> select /main:-14
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /main:-13
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /opp:18
31 atoms, 32 bonds, 1 residue, 1 model selected
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
> session
opened ChimeraX session
> close
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb
7jk3-dmODC_GCrich.pdb title:
Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...]
Chain information for 7jk3-dmODC_GCrich.pdb #1
---
Chain | Description | UniProt
A | DMORC1 | ORC1_DROME 440-924
B | DMORC2 | ORC2_DROME 1-618
C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721
D | ORC4 | Q9W102_DROME 1-459
E | ORC5 | ORC5_DROME 1-460
F | ORC6 | ORC6_DROME 1-257
G | CDC6 | Q9VSM9_DROME 242-662
H | DNA (33-mer) |
I | DNA (33-mer) |
Non-standard residues in 7jk3-dmODC_GCrich.pdb #1
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
> modelfix
Changed 21661 atom styles
20180 atoms, 20524 bonds, 18 pseudobonds, 2528 residues, 2 models selected
> close #1
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/hsORC1-6_CDC6_60bpDNA.pdb
> format pdb
Chain information for hsORC1-6_CDC6_60bpDNA.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 21416 atom styles
20099 atoms, 20484 bonds, 13 pseudobonds, 2485 residues, 2 models selected
Computing secondary structure
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb format
> pdb
7jk3-dmODC_GCrich.pdb title:
Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...]
Chain information for 7jk3-dmODC_GCrich.pdb #2
---
Chain | Description | UniProt
A | DMORC1 | ORC1_DROME 440-924
B | DMORC2 | ORC2_DROME 1-618
C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721
D | ORC4 | Q9W102_DROME 1-459
E | ORC5 | ORC5_DROME 1-460
F | ORC6 | ORC6_DROME 1-257
G | CDC6 | Q9VSM9_DROME 242-662
H | DNA (33-mer) |
I | DNA (33-mer) |
Non-standard residues in 7jk3-dmODC_GCrich.pdb #2
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
> modelfix
Changed 43077 atom styles
40279 atoms, 41008 bonds, 31 pseudobonds, 5013 residues, 4 models selected
> matchmaker #2 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain C (#1) with 7jk3-dmODC_GCrich.pdb,
chain C (#2), sequence alignment score = 1256.2
RMSD between 288 pruned atom pairs is 1.187 angstroms; (across all 575 pairs:
4.218)
> select #2/G:623
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #2/C:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide #!2 models
> hide #!1 models
> show #!1 models
> select add #2
21661 atoms, 22172 bonds, 30 pseudobonds, 2602 residues, 3 models selected
> select subtract #2
Nothing selected
> show #!2 models
> hide #!1 models
> select #2/C:711
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/C:712
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/C:710
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!2 models
> show #!2 models
> select clear
> matchmaker #2/D to #1/D
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain D (#1) with 7jk3-dmODC_GCrich.pdb,
chain D (#2), sequence alignment score = 1104.3
RMSD between 338 pruned atom pairs is 0.924 angstroms; (across all 410 pairs:
2.005)
> select #2/D:410
7 atoms, 6 bonds, 1 residue, 1 model selected
> matchmaker #2/E to #1/E
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1) with 7jk3-dmODC_GCrich.pdb,
chain E (#2), sequence alignment score = 853.4
RMSD between 290 pruned atom pairs is 1.201 angstroms; (across all 363 pairs:
2.631)
> select clear
> open /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7mca-assembly1.cif format
> mmcif
7mca-assembly1.cif title:
Structure of the S. cerevisiae origin recognition complex bound to the
replication initiator Cdc6 and the ARS1 origin DNA. [more info...]
Chain information for 7mca-assembly1.cif #3
---
Chain | Description
A | Origin recognition complex subunit 1
B | Origin recognition complex subunit 2
C | Origin recognition complex subunit 3
D | Origin recognition complex subunit 4
E | Origin recognition complex subunit 5
F | Origin recognition complex subunit 6
G | DNA (85-MER)
H | DNA (85-MER)
I | Cell division control protein 6
Non-standard residues in 7mca-assembly1.cif #3
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> modelfix
Changed 67769 atom styles
62793 atoms, 63953 bonds, 45 pseudobonds, 7773 residues, 6 models selected
> newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H
> matchmaker /A to #1/A
Must use different reference and match structures
> matchmaker #2-3/A to #1/A
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1) with 7jk3-dmODC_GCrich.pdb,
chain A (#2), sequence alignment score = 1245.5
RMSD between 341 pruned atom pairs is 0.995 angstroms; (across all 383 pairs:
1.387)
Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1) with 7mca-assembly1.cif,
chain A (#3), sequence alignment score = 707.9
RMSD between 295 pruned atom pairs is 1.089 angstroms; (across all 368 pairs:
4.720)
> matchmaker #2-3/B to #1/B
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1) with 7jk3-dmODC_GCrich.pdb,
chain B (#2), sequence alignment score = 879.5
RMSD between 201 pruned atom pairs is 1.032 angstroms; (across all 272 pairs:
2.378)
Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1) with 7mca-assembly1.cif,
chain B (#3), sequence alignment score = 458.2
RMSD between 130 pruned atom pairs is 0.873 angstroms; (across all 193 pairs:
3.624)
> hide #!2 models
> hide #!1 models
> select #3/C:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:159
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3
24692 atoms, 25375 bonds, 14 pseudobonds, 2868 residues, 2 models selected
> hide #!3 models
> select subtract #3
Nothing selected
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"
Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 93068 atom styles
86492 atoms, 88098 bonds, 54 pseudobonds, 10743 residues, 8 models selected
> newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H
> matchmaker #1-3/A to #4
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1), sequence alignment score = 965.4
RMSD between 213 pruned atom pairs is 1.228 angstroms; (across all 381 pairs:
3.152)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with
7jk3-dmODC_GCrich.pdb, chain A (#2), sequence alignment score = 962.2
RMSD between 250 pruned atom pairs is 1.152 angstroms; (across all 383 pairs:
6.101)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 943
RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
5.169)
> show #!3 models
> show #!2 models
> show #!1 models
> matchmaker #1-3/A to #4/A
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with
hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1), sequence alignment score = 965.4
RMSD between 213 pruned atom pairs is 1.228 angstroms; (across all 381 pairs:
3.152)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with
7jk3-dmODC_GCrich.pdb, chain A (#2), sequence alignment score = 962.2
RMSD between 250 pruned atom pairs is 1.152 angstroms; (across all 383 pairs:
6.101)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with 7mca-
assembly1.cif, chain A (#3), sequence alignment score = 943
RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
5.169)
> matchmaker #1-3/B to #4/B
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with
hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1), sequence alignment score = 635.5
RMSD between 137 pruned atom pairs is 1.099 angstroms; (across all 304 pairs:
5.531)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with
7jk3-dmODC_GCrich.pdb, chain B (#2), sequence alignment score = 558
RMSD between 135 pruned atom pairs is 0.988 angstroms; (across all 284 pairs:
5.027)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with 7mca-
assembly1.cif, chain B (#3), sequence alignment score = 609.7
RMSD between 153 pruned atom pairs is 1.065 angstroms; (across all 237 pairs:
4.405)
> select #3/B:396
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select #1/B:367
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:365
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/B:367@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:367
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> show #!4 models
> hide #!1 models
> select #4/B:150
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!3 models
> show #!2 models
> show #!1 models
> select #3/B:255
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:254
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!4 models
> hide #!2 models
> hide #!1 models
> select clear
> color #!3 byhetero
> show #!4 models
> matchmaker #1-3/E to #4/E
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with
hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1), sequence alignment score = 675
RMSD between 179 pruned atom pairs is 1.291 angstroms; (across all 379 pairs:
4.186)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with
7jk3-dmODC_GCrich.pdb, chain E (#2), sequence alignment score = 567.4
RMSD between 149 pruned atom pairs is 1.290 angstroms; (across all 374 pairs:
4.652)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with 7mca-
assembly1.cif, chain E (#3), sequence alignment score = 646.2
RMSD between 174 pruned atom pairs is 1.399 angstroms; (across all 417 pairs:
4.188)
> hide #!4 models
> select #3/E:366
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/E:363
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/E:360
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!4 models
> matchmaker #1-3/E to #4/E:307-end
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with
hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1), sequence alignment score = 281.2
RMSD between 99 pruned atom pairs is 0.965 angstroms; (across all 120 pairs:
3.490)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with
7jk3-dmODC_GCrich.pdb, chain E (#2), sequence alignment score = 198.4
RMSD between 96 pruned atom pairs is 1.015 angstroms; (across all 110 pairs:
1.673)
Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with 7mca-
assembly1.cif, chain E (#3), sequence alignment score = 312.4
RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
3.466)
> select #4/E:362
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/E:359
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/E:357
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/E:354
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!3 models
> select #4/E:355
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/E:354
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!3 models
> hide #!4 models
> select #3/E:363
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/E:358
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/E:439
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:369
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:367
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:365
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> close #3
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_024.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_023.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_022.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_021.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_020.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_019.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_018.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_017.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_016.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_015.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_014.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_013.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_012.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_011.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_010.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_009.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_008.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_007.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_006.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_005.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_004.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_003.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_002.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_001.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_000.mrc"
Opened J407_component_000_frame_024.mrc as #1.1, grid size 440,440,440, pixel
0.827, shown at level 0.0246, step 2, values float32
Opened J407_component_000_frame_023.mrc as #1.2, grid size 440,440,440, pixel
0.827, shown at level 0.0247, step 2, values float32
Opened J407_component_000_frame_022.mrc as #1.3, grid size 440,440,440, pixel
0.827, shown at level 0.0246, step 2, values float32
Opened J407_component_000_frame_021.mrc as #1.4, grid size 440,440,440, pixel
0.827, shown at level 0.0248, step 2, values float32
Opened J407_component_000_frame_020.mrc as #1.5, grid size 440,440,440, pixel
0.827, shown at level 0.025, step 2, values float32
Opened J407_component_000_frame_019.mrc as #1.6, grid size 440,440,440, pixel
0.827, shown at level 0.0253, step 2, values float32
Opened J407_component_000_frame_018.mrc as #1.7, grid size 440,440,440, pixel
0.827, shown at level 0.0256, step 2, values float32
Opened J407_component_000_frame_017.mrc as #1.8, grid size 440,440,440, pixel
0.827, shown at level 0.0259, step 2, values float32
Opened J407_component_000_frame_016.mrc as #1.9, grid size 440,440,440, pixel
0.827, shown at level 0.0262, step 2, values float32
Opened J407_component_000_frame_015.mrc as #1.10, grid size 440,440,440, pixel
0.827, shown at level 0.0265, step 2, values float32
Opened J407_component_000_frame_014.mrc as #1.11, grid size 440,440,440, pixel
0.827, shown at level 0.0267, step 2, values float32
Opened J407_component_000_frame_013.mrc as #1.12, grid size 440,440,440, pixel
0.827, shown at level 0.0268, step 2, values float32
Opened J407_component_000_frame_012.mrc as #1.13, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_000_frame_011.mrc as #1.14, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_000_frame_010.mrc as #1.15, grid size 440,440,440, pixel
0.827, shown at level 0.0268, step 2, values float32
Opened J407_component_000_frame_009.mrc as #1.16, grid size 440,440,440, pixel
0.827, shown at level 0.0266, step 2, values float32
Opened J407_component_000_frame_008.mrc as #1.17, grid size 440,440,440, pixel
0.827, shown at level 0.0265, step 2, values float32
Opened J407_component_000_frame_007.mrc as #1.18, grid size 440,440,440, pixel
0.827, shown at level 0.0263, step 2, values float32
Opened J407_component_000_frame_006.mrc as #1.19, grid size 440,440,440, pixel
0.827, shown at level 0.0261, step 2, values float32
Opened J407_component_000_frame_005.mrc as #1.20, grid size 440,440,440, pixel
0.827, shown at level 0.026, step 2, values float32
Opened J407_component_000_frame_004.mrc as #1.21, grid size 440,440,440, pixel
0.827, shown at level 0.0258, step 2, values float32
Opened J407_component_000_frame_003.mrc as #1.22, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_002.mrc as #1.23, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_001.mrc as #1.24, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_000.mrc as #1.25, grid size 440,440,440, pixel
0.827, shown at level 0.0258, step 2, values float32
> volume step 1
> volume level 0.1
> morph #1
Require at least 2 structures for morph
> morph #1.1-1.25
Require at least 2 structures for morph
> volume morph #1
Opened morph as #2, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> close #2
> vop flip #1
Opened J407_component_000_frame_024.mrc z flip as #2, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_023.mrc z flip as #3, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_022.mrc z flip as #4, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_021.mrc z flip as #5, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_020.mrc z flip as #6, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_019.mrc z flip as #7, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_018.mrc z flip as #8, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_017.mrc z flip as #9, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_016.mrc z flip as #10, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_015.mrc z flip as #11, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_014.mrc z flip as #12, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_013.mrc z flip as #13, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_012.mrc z flip as #14, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_011.mrc z flip as #15, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_010.mrc z flip as #16, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_009.mrc z flip as #17, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_008.mrc z flip as #18, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_007.mrc z flip as #19, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_006.mrc z flip as #20, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_005.mrc z flip as #21, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_004.mrc z flip as #22, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_003.mrc z flip as #23, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_002.mrc z flip as #24, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_001.mrc z flip as #25, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_000.mrc z flip as #26, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
> close #1
> color #808080
> color grey
> color lightgrey
> color darkgrey
> volume morph #2-26
Opened morph as #1, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> close #1
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_024.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_023.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_022.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_021.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_020.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_019.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_018.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_017.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_016.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_015.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_014.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_013.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_012.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_011.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_010.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_009.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_008.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_007.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_006.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_005.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_004.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_003.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_002.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_001.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J408_component_000/J408_component_000_frame_000.mrc"
Opened J408_component_000_frame_024.mrc as #1.1, grid size 440,440,440, pixel
0.827, shown at level 0.135, step 2, values float32
Opened J408_component_000_frame_023.mrc as #1.2, grid size 440,440,440, pixel
0.827, shown at level 0.112, step 2, values float32
Opened J408_component_000_frame_022.mrc as #1.3, grid size 440,440,440, pixel
0.827, shown at level 0.103, step 2, values float32
Opened J408_component_000_frame_021.mrc as #1.4, grid size 440,440,440, pixel
0.827, shown at level 0.0998, step 2, values float32
Opened J408_component_000_frame_020.mrc as #1.5, grid size 440,440,440, pixel
0.827, shown at level 0.0974, step 2, values float32
Opened J408_component_000_frame_019.mrc as #1.6, grid size 440,440,440, pixel
0.827, shown at level 0.0929, step 2, values float32
Opened J408_component_000_frame_018.mrc as #1.7, grid size 440,440,440, pixel
0.827, shown at level 0.0878, step 2, values float32
Opened J408_component_000_frame_017.mrc as #1.8, grid size 440,440,440, pixel
0.827, shown at level 0.0867, step 2, values float32
Opened J408_component_000_frame_016.mrc as #1.9, grid size 440,440,440, pixel
0.827, shown at level 0.092, step 2, values float32
Opened J408_component_000_frame_015.mrc as #1.10, grid size 440,440,440, pixel
0.827, shown at level 0.105, step 2, values float32
Opened J408_component_000_frame_014.mrc as #1.11, grid size 440,440,440, pixel
0.827, shown at level 0.128, step 2, values float32
Opened J408_component_000_frame_013.mrc as #1.12, grid size 440,440,440, pixel
0.827, shown at level 0.167, step 2, values float32
Opened J408_component_000_frame_012.mrc as #1.13, grid size 440,440,440, pixel
0.827, shown at level 0.216, step 2, values float32
Opened J408_component_000_frame_011.mrc as #1.14, grid size 440,440,440, pixel
0.827, shown at level 0.235, step 2, values float32
Opened J408_component_000_frame_010.mrc as #1.15, grid size 440,440,440, pixel
0.827, shown at level 0.205, step 2, values float32
Opened J408_component_000_frame_009.mrc as #1.16, grid size 440,440,440, pixel
0.827, shown at level 0.166, step 2, values float32
Opened J408_component_000_frame_008.mrc as #1.17, grid size 440,440,440, pixel
0.827, shown at level 0.143, step 2, values float32
Opened J408_component_000_frame_007.mrc as #1.18, grid size 440,440,440, pixel
0.827, shown at level 0.133, step 2, values float32
Opened J408_component_000_frame_006.mrc as #1.19, grid size 440,440,440, pixel
0.827, shown at level 0.128, step 2, values float32
Opened J408_component_000_frame_005.mrc as #1.20, grid size 440,440,440, pixel
0.827, shown at level 0.127, step 2, values float32
Opened J408_component_000_frame_004.mrc as #1.21, grid size 440,440,440, pixel
0.827, shown at level 0.124, step 2, values float32
Opened J408_component_000_frame_003.mrc as #1.22, grid size 440,440,440, pixel
0.827, shown at level 0.123, step 2, values float32
Opened J408_component_000_frame_002.mrc as #1.23, grid size 440,440,440, pixel
0.827, shown at level 0.125, step 2, values float32
Opened J408_component_000_frame_001.mrc as #1.24, grid size 440,440,440, pixel
0.827, shown at level 0.135, step 2, values float32
Opened J408_component_000_frame_000.mrc as #1.25, grid size 440,440,440, pixel
0.827, shown at level 0.154, step 2, values float32
> volume step 1
> volume level 0.1 #1
Expected a keyword
> vop level 0.2 #1
> volume level 0.2 #1
Expected a keyword
> vop level #1 0.2
> volume level #1 0.2
Invalid "level" argument: Expected a number
> vop level
> volume level
Missing "level" keyword's argument
> volume #1.10 level 0.12
> vop #1 level 0.2
> vop #1 level 0.3
> vop #1 level 0.2
> surface dust #1.1 size 8.27
> surface dust #1.2 size 8.27
> surface dust #1.3 size 8.27
> surface dust #1.4 size 8.27
> surface dust #1.5 size 8.27
> surface dust #1.6 size 8.27
> surface dust #1.7 size 8.27
> surface dust #1.8 size 8.27
> surface dust #1.9 size 8.27
> surface dust #1.10 size 8.27
> surface dust #1.11 size 8.27
> surface dust #1.12 size 8.27
> surface dust #1.13 size 8.27
> surface dust #1.14 size 8.27
> surface dust #1.15 size 8.27
> surface dust #1.16 size 8.27
> surface dust #1.17 size 8.27
> surface dust #1.18 size 8.27
> surface dust #1.19 size 8.27
> surface dust #1.20 size 8.27
> surface dust #1.21 size 8.27
> surface dust #1.22 size 8.27
> surface dust #1.23 size 8.27
> surface dust #1.24 size 8.27
> surface dust #1.25 size 8.27
> volume morph #1
Opened morph as #27, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> surface dust #27 size 8.27
> close #1
> close #27
> volume show
> volume hide
> volume morph #2-26
Opened morph as #1, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> hide #!1 models
> show #!26 models
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"
Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #27
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 25299 atom styles
23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected
> select /C:220
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #!1 models
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/cryosparc_P370_J380_005_volume_map.mrc"
Opened cryosparc_P370_J380_005_volume_map.mrc as #28, grid size 440,440,440,
pixel 0.827, shown at level 0.0231, step 2, values float32
> vop flip #28
Opened cryosparc_P370_J380_005_volume_map.mrc z flip as #29, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
> close #28
> volume #29 level 0.09557
> hide #!27 models
> select add #27
25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected
> select subtract #27
Nothing selected
> close #29
> close #27
> show #!1 models
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/J407_component0_ORC_OPEN-CLOSE.cxs"
> close #1
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_000.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_001.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_002.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_003.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_004.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_005.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_006.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_007.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_008.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_009.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_010.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_011.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_012.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_013.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_014.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_015.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_016.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_017.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_018.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_019.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_020.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_021.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_022.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_023.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_001/J407_component_001_frame_024.mrc"
Opened J407_component_001_frame_000.mrc as #1.1, grid size 440,440,440, pixel
0.827, shown at level 0.0267, step 2, values float32
Opened J407_component_001_frame_001.mrc as #1.2, grid size 440,440,440, pixel
0.827, shown at level 0.0266, step 2, values float32
Opened J407_component_001_frame_002.mrc as #1.3, grid size 440,440,440, pixel
0.827, shown at level 0.0265, step 2, values float32
Opened J407_component_001_frame_003.mrc as #1.4, grid size 440,440,440, pixel
0.827, shown at level 0.0264, step 2, values float32
Opened J407_component_001_frame_004.mrc as #1.5, grid size 440,440,440, pixel
0.827, shown at level 0.0264, step 2, values float32
Opened J407_component_001_frame_005.mrc as #1.6, grid size 440,440,440, pixel
0.827, shown at level 0.0263, step 2, values float32
Opened J407_component_001_frame_006.mrc as #1.7, grid size 440,440,440, pixel
0.827, shown at level 0.0264, step 2, values float32
Opened J407_component_001_frame_007.mrc as #1.8, grid size 440,440,440, pixel
0.827, shown at level 0.0264, step 2, values float32
Opened J407_component_001_frame_008.mrc as #1.9, grid size 440,440,440, pixel
0.827, shown at level 0.0264, step 2, values float32
Opened J407_component_001_frame_009.mrc as #1.10, grid size 440,440,440, pixel
0.827, shown at level 0.0265, step 2, values float32
Opened J407_component_001_frame_010.mrc as #1.11, grid size 440,440,440, pixel
0.827, shown at level 0.0266, step 2, values float32
Opened J407_component_001_frame_011.mrc as #1.12, grid size 440,440,440, pixel
0.827, shown at level 0.0266, step 2, values float32
Opened J407_component_001_frame_012.mrc as #1.13, grid size 440,440,440, pixel
0.827, shown at level 0.0267, step 2, values float32
Opened J407_component_001_frame_013.mrc as #1.14, grid size 440,440,440, pixel
0.827, shown at level 0.0268, step 2, values float32
Opened J407_component_001_frame_014.mrc as #1.15, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_001_frame_015.mrc as #1.16, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_001_frame_016.mrc as #1.17, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_001_frame_017.mrc as #1.18, grid size 440,440,440, pixel
0.827, shown at level 0.027, step 2, values float32
Opened J407_component_001_frame_018.mrc as #1.19, grid size 440,440,440, pixel
0.827, shown at level 0.0271, step 2, values float32
Opened J407_component_001_frame_019.mrc as #1.20, grid size 440,440,440, pixel
0.827, shown at level 0.0271, step 2, values float32
Opened J407_component_001_frame_020.mrc as #1.21, grid size 440,440,440, pixel
0.827, shown at level 0.0272, step 2, values float32
Opened J407_component_001_frame_021.mrc as #1.22, grid size 440,440,440, pixel
0.827, shown at level 0.0273, step 2, values float32
Opened J407_component_001_frame_022.mrc as #1.23, grid size 440,440,440, pixel
0.827, shown at level 0.0273, step 2, values float32
Opened J407_component_001_frame_023.mrc as #1.24, grid size 440,440,440, pixel
0.827, shown at level 0.0275, step 2, values float32
Opened J407_component_001_frame_024.mrc as #1.25, grid size 440,440,440, pixel
0.827, shown at level 0.0276, step 2, values float32
> vop flip #1
Opened J407_component_001_frame_000.mrc z flip as #2, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_001.mrc z flip as #3, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_002.mrc z flip as #4, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_003.mrc z flip as #5, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_004.mrc z flip as #6, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_005.mrc z flip as #7, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_006.mrc z flip as #8, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_007.mrc z flip as #9, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_008.mrc z flip as #10, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_009.mrc z flip as #11, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_010.mrc z flip as #12, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_011.mrc z flip as #13, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_012.mrc z flip as #14, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_013.mrc z flip as #15, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_014.mrc z flip as #16, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_015.mrc z flip as #17, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_016.mrc z flip as #18, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_017.mrc z flip as #19, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_018.mrc z flip as #20, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_019.mrc z flip as #21, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_020.mrc z flip as #22, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_021.mrc z flip as #23, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_022.mrc z flip as #24, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_023.mrc z flip as #25, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_001_frame_024.mrc z flip as #26, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
> vop level 0.1
> hide #!1 models
> vop morph #2-26
Opened morph as #27, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/cryosparc_P370_J339_component_002.zip"
Unrecognized file suffix '.zip'
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_000.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_001.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_002.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_003.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_004.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_005.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_006.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_007.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_008.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_009.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_010.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_011.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_012.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_013.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_014.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_015.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_016.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_017.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_018.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J339_component_002/J339_component_002_frame_019.mrc"
Opened J339_component_002_frame_000.mrc as #1.1, grid size 440,440,440, pixel
0.827, shown at level 0.0255, step 2, values float32
Opened J339_component_002_frame_001.mrc as #1.2, grid size 440,440,440, pixel
0.827, shown at level 0.0253, step 2, values float32
Opened J339_component_002_frame_002.mrc as #1.3, grid size 440,440,440, pixel
0.827, shown at level 0.0252, step 2, values float32
Opened J339_component_002_frame_003.mrc as #1.4, grid size 440,440,440, pixel
0.827, shown at level 0.025, step 2, values float32
Opened J339_component_002_frame_004.mrc as #1.5, grid size 440,440,440, pixel
0.827, shown at level 0.0248, step 2, values float32
Opened J339_component_002_frame_005.mrc as #1.6, grid size 440,440,440, pixel
0.827, shown at level 0.0248, step 2, values float32
Opened J339_component_002_frame_006.mrc as #1.7, grid size 440,440,440, pixel
0.827, shown at level 0.0247, step 2, values float32
Opened J339_component_002_frame_007.mrc as #1.8, grid size 440,440,440, pixel
0.827, shown at level 0.0246, step 2, values float32
Opened J339_component_002_frame_008.mrc as #1.9, grid size 440,440,440, pixel
0.827, shown at level 0.0247, step 2, values float32
Opened J339_component_002_frame_009.mrc as #1.10, grid size 440,440,440, pixel
0.827, shown at level 0.0247, step 2, values float32
Opened J339_component_002_frame_010.mrc as #1.11, grid size 440,440,440, pixel
0.827, shown at level 0.0248, step 2, values float32
Opened J339_component_002_frame_011.mrc as #1.12, grid size 440,440,440, pixel
0.827, shown at level 0.0249, step 2, values float32
Opened J339_component_002_frame_012.mrc as #1.13, grid size 440,440,440, pixel
0.827, shown at level 0.025, step 2, values float32
Opened J339_component_002_frame_013.mrc as #1.14, grid size 440,440,440, pixel
0.827, shown at level 0.0252, step 2, values float32
Opened J339_component_002_frame_014.mrc as #1.15, grid size 440,440,440, pixel
0.827, shown at level 0.0253, step 2, values float32
Opened J339_component_002_frame_015.mrc as #1.16, grid size 440,440,440, pixel
0.827, shown at level 0.0254, step 2, values float32
Opened J339_component_002_frame_016.mrc as #1.17, grid size 440,440,440, pixel
0.827, shown at level 0.0256, step 2, values float32
Opened J339_component_002_frame_017.mrc as #1.18, grid size 440,440,440, pixel
0.827, shown at level 0.0258, step 2, values float32
Opened J339_component_002_frame_018.mrc as #1.19, grid size 440,440,440, pixel
0.827, shown at level 0.0259, step 2, values float32
Opened J339_component_002_frame_019.mrc as #1.20, grid size 440,440,440, pixel
0.827, shown at level 0.0261, step 2, values float32
> vop flip #1
Opened J339_component_002_frame_000.mrc z flip as #2, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_001.mrc z flip as #3, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_002.mrc z flip as #4, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_003.mrc z flip as #5, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_004.mrc z flip as #6, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_005.mrc z flip as #7, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_006.mrc z flip as #8, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_007.mrc z flip as #9, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_008.mrc z flip as #10, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_009.mrc z flip as #11, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_010.mrc z flip as #12, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_011.mrc z flip as #13, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_012.mrc z flip as #14, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_013.mrc z flip as #15, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_014.mrc z flip as #16, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_015.mrc z flip as #17, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_016.mrc z flip as #18, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_017.mrc z flip as #19, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_018.mrc z flip as #20, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_019.mrc z flip as #21, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
> vop level 0.1
> hide #!1 models
> vop morph #2-21
Opened morph as #22, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> show #!21 models
> hide #!22 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!21 models
> hide #!20 models
> hide #!21 models
> close #22
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_45bp-
> oriC061_complete/ODC1-6_45bpOriC061_DNApucker_rev3.cif"
Summary of feedback from opening /Users/jtbauer/Library/CloudStorage/OneDrive-
Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
structures/PDBs/ylODC_45bp-
oriC061_complete/ODC1-6_45bpOriC061_DNApucker_rev3.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 19
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for ODC1-6_45bpOriC061_DNApucker_rev3.cif #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 25273 atom styles
23792 atoms, 24240 bonds, 9 pseudobonds, 2982 residues, 2 models selected
Computing secondary structure
> lighting soft
> graphics silhouettes true
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/45bp_too_short.png" supersample 3 transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
> set bgColor white
> graphics silhouettes true
> alias newcolor color $1 darkseagreen ; color $2 burlywood ; color $3 coral ;
> color $4 #498cff ; color $5 mediumslateblue ; color $6 grey ; color $7
> #ff69b4 ; color $8 #20B2AA ; color $9 #20B2AA
> alias propercolor color $1 mediumslateblue ; color $2 lightcoral ; color $3
> darkseagreen ; color $4 burlywood ; color $5 coral ; color $6 grey ; color
> $7 #bb57a1ff ; color $8 #0080ffff ; color $9 #004080ff
> alias removeatom select main ; style stick ; color sel byhetero ; hide sel
> atoms ; show sel cartoons ; select clear
> alias showATP select ::name="ATP" ; show sel ; color sel byhetero ; select
> clear
> alias modelfix style stick ; newcolor /A /B /C /D /E /F /G /H /I ; color
> byhetero ; show cartoons ; select clear ; select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
> ; hide sel atoms ; select clear
> lighting soft
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: Z176000HCLL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 11881.61.3
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.2 (23H311)
Kernel Version: Darwin 23.6.0
Time since boot: 51 days, 21 hours, 52 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
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